Merge pull request #2 from molssi-seamm/dev

Added geomeTRIC minimizer

HISTORY.rst

@@ -2,7 +2,10 @@
 History
 =======
 
-2024.7.31 (2024-07-31)
-----------------------
+2024.10.13 -- Added geomeTRIC minimizer
+    * Added transition states as a target
+    * Added the geomeTRIC minimizer
+    * Rationalized the convergence criteria, allowing them to be used across minimizers.
+
+2024.7.31 -- Plug-in created using the SEAMM plug-in cookiecutter.
 
-* Plug-in created using the SEAMM plug-in cookiecutter.

devtools/conda-envs/test_env.yaml

@@ -26,6 +26,7 @@ dependencies:
   # Pip-only installs
   - pip:
     - seamm-ase
+    - seamm-geometric
     # Documentation
     - sphinx-copybutton
     - sphinxnotes-strike

requirements.txt

@@ -1,5 +1,6 @@
 seamm
 seamm-ase
+seamm-geometric
 seamm-util
 seamm-widgets
 tabulate

structure_step/metadata.py

@@ -5,6 +5,231 @@
 
 metadata = {}
 
+# Optimizers
+metadata["optimizers"] = {
+    "geomeTRIC/geomeTRIC": {
+        "convergence formulas": (
+            "E+grad+step",
+            "ASE",
+            "MolPro",
+            "MOPAC",
+            "QChem",
+        ),
+        "coordinate systems": (
+            "TRIC: translation-rotation internal coordinates",
+            "TRIC-p: primitive (redundant) TRIC",
+            "Cart: Cartesian coordinates",
+            "DLC: delocalized internal coordinates",
+            "HDLC: hybrid delocalized internal coordinates",
+        ),
+        "targets": (
+            "minimum",
+            "transition state",
+        ),
+        "default": True,
+    },
+    "BFGS/ASE": {
+        "convergence formulas": ("ASE",),
+        "targets": ("minimum",),
+    },
+    "BFGSLineSearch/ASE": {
+        "convergence formulas": ("ASE",),
+        "targets": ("minimum",),
+    },
+    "LBFGS/ASE": {
+        "convergence formulas": ("ASE",),
+        "targets": ("minimum",),
+    },
+    "LBFGSLineSearch/ASE": {
+        "convergence formulas": ("ASE",),
+        "targets": ("minimum",),
+    },
+    "GPMin/ASE": {
+        "convergence formulas": ("ASE",),
+        "targets": ("minimum",),
+    },
+    "MDMin/ASE": {
+        "convergence formulas": ("ASE",),
+        "targets": ("minimum",),
+    },
+    "FIRE/ASE": {
+        "convergence formulas": ("ASE",),
+        "targets": ("minimum",),
+    },
+}
+
+# The various formulas for convergence criteria
+metadata["convergence formulas"] = {
+    "E+grad+step": {
+        "text": (
+            "  _energy change_ < Energy change criterion          \n"
+            "   _rms gradient_ < RMS gradient criterion           \n"
+            "_atomic gradient_ < Maximum atomic gradient criterion\n"
+            "       _rms step_ < RMS step criterion               \n"
+            "    _atomic step_ < Maximum atomic step criterion    "
+        ),
+        "criteria": (
+            "Energy change criterion",
+            "RMS gradient criterion",
+            "Maximum atomic gradient criterion",
+            "RMS step criterion",
+            "Maximum atomic step criterion",
+        ),
+    },
+    "ASE": {
+        "text": "_atomic gradient_ < Maximum atomic gradient criterion",
+        "criteria": ("Maximum atomic gradient criterion",),
+    },
+    "MolPro": {
+        "text": (
+            "_atomic gradient_ < Maximum atomic gradient criterion\n"
+            "and\n"
+            "  _energy change_ < Energy change criterion          \n"
+            "or\n"
+            "    _atomic step_ < Maximum atomic step criterion    "
+        ),
+        "criteria": (
+            "Energy change criterion",
+            "Maximum atomic gradient criterion",
+            "Maximum atomic step criterion",
+        ),
+    },
+    "MOPAC": {
+        "text": "_rms gradient_ < RMS gradient criterion",
+        "criteria": ("RMS gradient criterion",),
+    },
+    "QChem": {
+        "text": (
+            "_atomic gradient_ < Maximum atomic gradient criterion\n"
+            "and\n"
+            "  _energy change_ < Energy change criterion          \n"
+            "or\n"
+            "    _atomic step_ < Maximum atomic step criterion    "
+        ),
+        "criteria": (
+            "Energy change criterion",
+            "Maximum atomic gradient criterion",
+            "Maximum atomic step criterion",
+        ),
+    },
+}
+
+# The convergence criteria
+metadata["convergence parameters"] = {
+    "ASE": {
+        "Energy change criterion": ("99.9", "E_h"),
+        "RMS gradient criterion": ("99.9", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("0.05", "eV/Å"),
+        "RMS step criterion": ("99.9", "Å"),
+        "Maximum atomic step criterion": ("99.9", "Å"),
+        "convergence formula": "ASE",
+    },
+    "Gaussian (loose)": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("1.7e-4", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("2.5e-3", "E_h/Å"),
+        "RMS step criterion": ("6.7e-3", "Å"),
+        "Maximum atomic step criterion": ("1.0e-2", "Å"),
+        "convergence formula": "E+grad+step",
+    },
+    "Gaussian": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("3.0e-4", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("4.5e-4", "E_h/Å"),
+        "RMS step criterion": ("1.2e-3", "Å"),
+        "Maximum atomic step criterion": ("1.8e-3", "Å"),
+        "convergence formula": "E+grad+step",
+    },
+    "Gaussian (tight)": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("1.0e-6", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("2.0e-6", "E_h/Å"),
+        "RMS step criterion": ("4.0e-5", "Å"),
+        "Maximum atomic step criterion": ("6.0e-5", "Å"),
+        "convergence formula": "E+grad+step",
+    },
+    "Gaussian (very tight)": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("1.0e-6", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("2.0e-6", "E_h/Å"),
+        "RMS step criterion": ("4.0e-6", "Å"),
+        "Maximum atomic step criterion": ("6.0e-6", "Å"),
+        "convergence formula": "E+grad+step",
+    },
+    "Inter-fragment (tight)": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("1.0e-5", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("1.5e-5", "E_h/Å"),
+        "RMS step criterion": ("4.0e-4", "Å"),
+        "Maximum atomic step criterion": ("6.0e-4", "Å"),
+        "convergence formula": "E+grad+step",
+    },
+    "MolPro": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("99.9", "E_h/a_0"),
+        "Maximum atomic gradient criterion": ("3.0e-4", "E_h/a_0"),
+        "RMS step criterion": ("99.9", "a_0"),
+        "Maximum atomic step criterion": ("3.0e-4", "a_0"),
+        "convergence formula": "MolPro",
+    },
+    "MOPAC": {
+        "Energy change criterion": ("99.9", "kcal/mol"),
+        "RMS gradient criterion": ("1.0", "kcal/mol/Å"),
+        "Maximum atomic gradient criterion": ("99.9", "kcal/mol/Å"),
+        "RMS step criterion": ("99.9", "Å"),
+        "Maximum atomic step criterion": ("99.9", "Å"),
+        "convergence formula": "MOPAC",
+    },
+    "MOPAC (precise)": {
+        "Energy change criterion": ("99.9", "kcal/mol"),
+        "RMS gradient criterion": ("0.01", "kcal/mol/Å"),
+        "Maximum atomic gradient criterion": ("99.9", "kcal/mol/Å"),
+        "RMS step criterion": ("99.9", "Å"),
+        "Maximum atomic step criterion": ("99.9", "Å"),
+        "convergence formula": "MOPAC",
+    },
+    "NWChem (loose)": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("3.0e-3", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("4.5e-3", "E_h/Å"),
+        "RMS step criterion": ("3.6e-3", "Å"),
+        "Maximum atomic step criterion": ("5.4e-3", "Å"),
+        "convergence formula": "E+grad+step",
+    },
+    "NWChem": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("3.0e-4", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("4.5e-4", "E_h/Å"),
+        "RMS step criterion": ("1.2e-3", "Å"),
+        "Maximum atomic step criterion": ("1.8e-3", "Å"),
+        "convergence formula": "E+grad+step",
+    },
+    "NWChem (tight)": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("1.0e-6", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("2.0e-6", "E_h/Å"),
+        "RMS step criterion": ("4.0e-5", "Å"),
+        "Maximum atomic step criterion": ("6.0e-5", "Å"),
+        "convergence formula": "E+grad+step",
+    },
+    "QChem": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("99.9", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("3.0e-4", "E_h/Å"),
+        "RMS step criterion": ("99.9", "Å"),
+        "Maximum atomic step criterion": ("1.2e-3", "Å"),
+        "convergence formula": "QChem",
+    },
+    "Turbomole": {
+        "Energy change criterion": ("1.0e-6", "E_h"),
+        "RMS gradient criterion": ("5.0e-4", "E_h/Å"),
+        "Maximum atomic gradient criterion": ("1.0e-3", "E_h/Å"),
+        "RMS step criterion": ("5.0e-4", "Å"),
+        "Maximum atomic step criterion": ("1.0e-3", "Å"),
+        "convergence formula": "E+grad+step",
+    },
+}
+
 """Description of the computational models for Structure.
 
 Hamiltonians, approximations, and basis set or parameterizations,