Added CI calculations and better handling of transition states

HISTORY.rst

@@ -1,6 +1,13 @@
 =======
 History
 =======
+2024.8.17 --
+  * Added ability to do the various types of CI calculations that MOPAC supports.
+  * Improved the handling of TS calculations and added NLLSQ and SIGMA methods in
+    the optimization step.
+  * Added option to correctly handle transition states in the thermodynamics step and
+    improved the output to include the imaginary and low-lying frequencies.
+
 2024.7.29 -- Bugfix in bond analysis for atoms and mopac.ini
   * Fixed a bug in the bond analysis that caused the code to crash for calculations on
     atoms. 

mopac_step/energy_parameters.py

@@ -67,6 +67,21 @@ class EnergyParameters(seamm.Parameters):
             "description": "Hamiltonian:",
             "help_text": ("The Hamiltonian (parameterization) to use."),
         },
+        "calculation": {
+            "default": "HF: Hartree-Fock",
+            "kind": "enumeration",
+            "default_units": "",
+            "enumeration": (
+                "HF: Hartree-Fock",
+                "CASCI: Complete active space CI",
+                "CIS: CI with singles",
+                "CISD: CI with singles and doubles",
+                "CISDT: CI with singles, doubles, and triples",
+            ),
+            "format_string": "s",
+            "description": "Calculation:",
+            "help_text": ("The type of calculation."),
+        },
         "convergence": {
             "default": "normal",
             "kind": "enumeration",
@@ -104,6 +119,45 @@ class EnergyParameters(seamm.Parameters):
             "description": "UHF for singlets:",
             "help_text": "Whether to use UHF for singlet states.",
         },
+        "number ci orbitals": {
+            "default": 2,
+            "kind": "integer",
+            "default_units": "",
+            "enumeration": tuple(),
+            "format_string": "",
+            "description": "Number of orbitals in CI:",
+            "help_text": "The number of orbitals to use in the CI.",
+        },
+        "number doubly occupied ci orbitals": {
+            "default": "default",
+            "kind": "integer",
+            "default_units": "",
+            "enumeration": ("default",),
+            "format_string": "",
+            "description": "Number of doubly occupied orbitals in CI:",
+            "help_text": "The number of doubly occupied orbitals to use in the CI.",
+        },
+        "ci root": {
+            "default": 1,
+            "kind": "integer",
+            "default_units": "",
+            "enumeration": tuple(),
+            "format_string": "",
+            "description": "CI root:",
+            "help_text": "The root to use in the CI.",
+        },
+        "print ci details": {
+            "default": "yes",
+            "kind": "boolean",
+            "default_units": "",
+            "enumeration": (
+                "yes",
+                "no",
+            ),
+            "format_string": "s",
+            "description": "Print the details of CI:",
+            "help_text": "Print the details of the CI.",
+        },
         "COSMO": {
             "default": "no",
             "kind": "boolean",

mopac_step/optimization.py

@@ -54,6 +54,12 @@ def description_text(self, P=None):
             text += "BFGS method."
         elif P["method"][0:5] == "L-BFGS":
             text += "L-BFGS small memory version of the BFGS method."
+        elif P["method"].startswith("TS"):
+            text += "EF method for a transition state."
+        elif P["method"].startswith("SIGMA"):
+            text += "McIver-Komornicki method for transition states."
+        elif P["method"].startswith("NLLSQ"):
+            text += "Bartel's method of nonlinear least squares of the gradient."
         else:
             text += "optimization method determined at runtime by '{method}'."
 
@@ -79,7 +85,7 @@ def description_text(self, P=None):
             text += " The geometrical convergence is {gnorm}."
 
         # Put in the description of the energy calculation
-        text += "\n\nThe energy and forces will be c" + energy_description[1:]
+        text += "\n\n" + energy_description
         text += "\n\n"
 
         if self.is_expr(P["hamiltonian"]):

mopac_step/thermodynamics.py

@@ -75,12 +75,23 @@ def description_text(self, P=None):
             "\nThe thermodynamics functions will be calculated from "
             "{Tmin} to {Tmax} in steps of {Tstep}. {trans} lowest "
             "modes will be ignored to approximately account for {trans} "
-            "internal rotations.\n\n"
+            "internal rotations."
         )
+        ts = P["transition state"]
+        if isinstance(ts, bool) and ts:
+            text += (
+                " Since the structure is a transition state, the lowest mode -- "
+                "the imaginary frequency -- will be ignored."
+            )
+        if isinstance(ts, str) and ts == "yes":
+            text += (
+                " Since the structure is a transition state, the lowest mode -- "
+                "the imaginary frequency -- will be ignored."
+            )
+        text += "\n\n"
 
         # Put in the description of the energy calculation
-        text += "\n\nThe energy and forces will be c" + energy_description[1:]
-        text += "\n\n"
+        text += energy_description + "\n\n"
 
         # Structure handling
         text += "The structure in the standard orientation will {structure handling} "
@@ -130,7 +141,11 @@ def get_input(self):
         if "1SCF" in keywords:
             keywords.remove("1SCF")
         keywords.append("THERMO=({Tmin},{Tmax},{Tstep})".format(**P))
-        keywords.append("TRANS={trans}".format(**P))
+        trans = P["trans"]
+        if P["transition state"]:
+            trans += 1
+        if trans > 0:
+            keywords.append(f"TRANS={trans}")
 
         return inputs
 
@@ -211,6 +226,69 @@ def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
                 message = "Error creating the cif file\n\n" + traceback.format_exc()
                 logger.warning(message)
 
+        # First, how many rotations are there?
+        n_rot = sum([0 if PMI < 0.001 else 1 for PMI in data["PRI_MOM_OF_I"]])
+        n_vib = len(data["VIB._FREQ"]) - 3 - n_rot
+
+        # Check for imaginary frequencies
+        imaginary = []
+        low = []
+        for frequency in data["VIB._FREQ"][0:n_vib]:
+            if frequency < 0:
+                imaginary.append(frequency)
+            elif frequency < 100:
+                low.append(frequency)
+
+        n_trans = P["trans"]
+
+        text_lines = ""
+
+        if len(imaginary) > 0:
+            tmp = [f"{-f:.1f}i" for f in imaginary]
+            tmp = ", ".join(tmp)
+            if len(imaginary) == 1:
+                text_lines += (
+                    textwrap.fill(
+                        "The structure is a transition state with one-mode with an "
+                        f"imaginary frequency of {tmp} cm^-1."
+                    )
+                    + "\n\n"
+                )
+            else:
+                text_lines += (
+                    textwrap.fill(
+                        "The structure is a more general saddle point with "
+                        f"{len(imaginary)} modes with imaginary frequencies: "
+                        f"{tmp} cm^-1."
+                    )
+                    + "\n\n"
+                )
+
+        if n_trans > 0:
+            tmp = [f"{-f:.1f}" for f in low[0:n_trans]]
+            tmp = ", ".join(tmp)
+            text_lines += (
+                textwrap.fill(
+                    f"You asked that {n_trans} low-lying modes be ignored: {tmp} cm^-1."
+                    " These should correspond to (almost) free rotors."
+                )
+                + "\n\n"
+            )
+            low = low[n_trans:]
+
+        if len(low) > 0:
+            tmp = [f"{f:.1f}" for f in low]
+            tmp = ", ".join(tmp)
+            text_lines += (
+                textwrap.fill(
+                    f"The structure has {len(low)} low-frequency modes: {tmp} cm^-1. "
+                    "You may wish to exclude these from the thermodynamics if they are "
+                    "(almost) free rotors that should not be handled within the "
+                    "harmonic approximation."
+                )
+                + "\n\n"
+            )
+
         # Print the moments of inertia
         p1, p2, p3 = data["PRI_MOM_OF_I"]
         r1, r2, r3 = data["ROTAT_CONSTS"]
@@ -221,7 +299,7 @@ def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
             "3": (p3, r3),
             "Units": ("1.0E-40 g.cm^2", "1/cm"),
         }
-        text_lines = "                  Rotational Constants\n"
+        text_lines += "                  Rotational Constants\n"
         text_lines += tabulate(
             tbl,
             headers="keys",
@@ -261,9 +339,6 @@ def analyze(self, indent="", data_sections=[], out_sections=[], table=None):
                 writer.writerow(row)
 
         # And the vibrational modes to a csv file
-        # First, how many rotations are there?
-        n_rot = sum([0 if PMI < 0.001 else 1 for PMI in data["PRI_MOM_OF_I"]])
-        n_vib = len(data["VIB._FREQ"]) - 3 - n_rot
         with open(directory / "vibrations.csv", "w", newline="") as fd:
             writer = csv.writer(fd)
             writer.writerow(

mopac_step/thermodynamics_parameters.py

@@ -58,6 +58,15 @@ class ThermodynamicsParameters(mopac_step.EnergyParameters):
                 "will be ignored, which is a first approximation."
             ),
         },
+        "transition state": {
+            "default": "no",
+            "kind": "boolean",
+            "default_units": "",
+            "enumeration": ("yes", "no"),
+            "format_string": "",
+            "description": "Transition state?:",
+            "help_text": "Whether this is a transition state.",
+        },
     }
 
     def __init__(self, defaults={}, data=None):

mopac_step/tk_energy.py

@@ -76,7 +76,7 @@ def create_dialog(self, title="Edit MOPAC Energy Step"):
                 self[key] = P[key].widget(e_frame)
 
         # Set the callbacks for changes
-        for widget in ("convergence", "MOZYME", "COSMO"):
+        for widget in ("calculation", "convergence", "MOZYME", "COSMO"):
             w = self[widget]
             w.combobox.bind("<<ComboboxSelected>>", self.reset_energy_frame)
             w.combobox.bind("<Return>", self.reset_energy_frame)
@@ -112,13 +112,25 @@ def reset_energy_frame(self, widget=None):
         for slave in frame.grid_slaves():
             slave.grid_forget()
 
+        calculation = self["calculation"].get()
         convergence = self["convergence"].get()
         cosmo = self["COSMO"].get()
         mozyme = self["MOZYME"].get()
 
         widgets = []
         row = 0
-        for key in ("hamiltonian", "uhf", "convergence"):
+        for key in ("hamiltonian", "calculation"):
+            self[key].grid(row=row, column=0, columnspan=2, sticky=tk.EW)
+            widgets.append(self[key])
+            row += 1
+
+        if "hf" in calculation.lower():
+            for key in ("uhf",):
+                self[key].grid(row=row, column=0, columnspan=2, sticky=tk.EW)
+                widgets.append(self[key])
+                row += 1
+
+        for key in ("convergence",):
             self[key].grid(row=row, column=0, columnspan=2, sticky=tk.EW)
             widgets.append(self[key])
             row += 1
@@ -137,19 +149,31 @@ def reset_energy_frame(self, widget=None):
             row += 1
             sw.align_labels((self["relative"], self["absolute"]), sticky=tk.E)
 
-        self["MOZYME"].grid(row=row, column=0, columnspan=2, sticky=tk.EW)
-        widgets.append(self["MOZYME"])
-        row += 1
-        subwidgets = []
-        if mozyme != "always" and mozyme != "never":
-            self["nMOZYME"].grid(row=row, column=1, sticky=tk.W)
-            subwidgets.append(self["nMOZYME"])
-            row += 1
-        if mozyme != "never":
-            self["MOZYME follow-up"].grid(row=row, column=1, sticky=tk.W)
-            subwidgets.append(self["MOZYME"])
+        if "hf" in calculation.lower():
+            self["MOZYME"].grid(row=row, column=0, columnspan=2, sticky=tk.EW)
+            widgets.append(self["MOZYME"])
             row += 1
-        sw.align_labels(subwidgets, sticky=tk.E)
+            subwidgets = []
+            if mozyme != "always" and mozyme != "never":
+                self["nMOZYME"].grid(row=row, column=1, sticky=tk.W)
+                subwidgets.append(self["nMOZYME"])
+                row += 1
+            if mozyme != "never":
+                self["MOZYME follow-up"].grid(row=row, column=1, sticky=tk.W)
+                subwidgets.append(self["MOZYME"])
+                row += 1
+            sw.align_labels(subwidgets, sticky=tk.E)
+
+        if "ci" in calculation.lower():
+            for key in (
+                "number ci orbitals",
+                "number doubly occupied ci orbitals",
+                "ci root",
+                "print ci details",
+            ):
+                self[key].grid(row=row, column=0, columnspan=2, sticky=tk.EW)
+                widgets.append(self[key])
+                row += 1
 
         self["COSMO"].grid(row=row, column=0, columnspan=2, sticky=tk.EW)
         widgets.append(self["COSMO"])

mopac_step/tk_optimization.py

@@ -112,7 +112,7 @@ def reset_optimization_frame(self, widget=None):
             self["gnorm"].grid(row=row, column=1, sticky=tk.EW)
             widgets_2.append(self["gnorm"])
             row += 1
-        if method[0:2] == "EF" or method[0] == "$":
+        if method.startswith("EF") or method.startswith("TS") or self.is_expr(method):
             self["recalc"].grid(row=row, column=1, sticky=tk.EW)
             widgets_2.append(self["recalc"])
             row += 1