From 6970ae0bfcbac28faeec034c5b72bb61b65b04cd Mon Sep 17 00:00:00 2001 From: Grant Hill Date: Thu, 30 Mar 2023 10:34:30 +0100 Subject: [PATCH 01/11] Tightens accuracy for multi molecule example --- .../{multi-molecule.py => multi_molecule.py} | 5 +++-- examples/multi-molecule/opt_basis.txt | 16 ++++++++-------- 2 files changed, 11 insertions(+), 10 deletions(-) rename examples/multi-molecule/{multi-molecule.py => multi_molecule.py} (85%) diff --git a/examples/multi-molecule/multi-molecule.py b/examples/multi-molecule/multi_molecule.py similarity index 85% rename from examples/multi-molecule/multi-molecule.py rename to examples/multi-molecule/multi_molecule.py index 2749afe..5664dc7 100644 --- a/examples/multi-molecule/multi-molecule.py +++ b/examples/multi-molecule/multi_molecule.py @@ -11,7 +11,8 @@ mol_objs = [bo.molecule.Molecule.from_xyz(mol + '.xyz', name=mol) for mol in list_of_mols] mb = MolecularBasis(name="double", molecules=mol_objs) -params = {'functional': "wb97x-d", 'scf_type': "pk"} +params = {'functional': "wb97x-d", 'scf_type': "pk", 'dft_spherical_points': "974", + 'dft_radial_points': "175", 'dft_pruning_scheme': "none"} strategy = Strategy() strategy.params = params @@ -31,7 +32,7 @@ bo_logger.info("Starting consistency iteration %d", counter + 1) mb.optimize() e_opt.append(strategy.last_objective) - e_diff = strategy.delta_objective + e_diff = abs(strategy.last_objective - e_opt[counter]) bo_logger.info("Objective function difference from previous iteration: %f\n", e_diff) counter += 1 diff --git a/examples/multi-molecule/opt_basis.txt b/examples/multi-molecule/opt_basis.txt index fcebbeb..017e6ce 100644 --- a/examples/multi-molecule/opt_basis.txt +++ b/examples/multi-molecule/opt_basis.txt @@ -2,16 +2,16 @@ spherical basis={ ! ! hydrogen (4s,1p) -> [4s,1p] -s, H , 1.797959e+01, 2.758758e+00, 6.245358e-01, 1.517951e-01 +s, H , 1.798531e+01, 2.759596e+00, 6.247444e-01, 1.517825e-01 c, 1.1, 1.000000e+00 c, 2.2, 1.000000e+00 c, 3.3, 1.000000e+00 c, 4.4, 1.000000e+00 -p, H , 8.438481e-01 +p, H , 8.446020e-01 c, 1.1, 1.000000e+00 ! ! carbon (7s,4p,1d) -> [7s,4p,1d] -s, C , 2.958169e+03, 4.440114e+02, 1.011358e+02, 2.862702e+01, 9.097819e+00, 3.047830e+00, 4.275333e-01 +s, C , 2.958325e+03, 4.440341e+02, 1.011409e+02, 2.862842e+01, 9.098225e+00, 3.047955e+00, 4.275739e-01 c, 1.1, 1.000000e+00 c, 2.2, 1.000000e+00 c, 3.3, 1.000000e+00 @@ -19,16 +19,16 @@ c, 4.4, 1.000000e+00 c, 5.5, 1.000000e+00 c, 6.6, 1.000000e+00 c, 7.7, 1.000000e+00 -p, C , 1.337480e+01, 3.008887e+00, 8.123437e-01, 2.404405e-01 +p, C , 1.337360e+01, 3.008598e+00, 8.122578e-01, 2.403973e-01 c, 1.1, 1.000000e+00 c, 2.2, 1.000000e+00 c, 3.3, 1.000000e+00 c, 4.4, 1.000000e+00 -d, C , 8.322163e-01 +d, C , 8.324954e-01 c, 1.1, 1.000000e+00 ! ! oxygen (7s,4p,1d) -> [7s,4p,1d] -s, O , 2.309354e+03, 3.473414e+02, 7.891545e+01, 2.185828e+01, 6.678970e+00, 1.004907e+00, 2.891048e-01 +s, O , 2.309352e+03, 3.473404e+02, 7.891515e+01, 2.185820e+01, 6.678948e+00, 1.004889e+00, 2.890962e-01 c, 1.1, 1.000000e+00 c, 2.2, 1.000000e+00 c, 3.3, 1.000000e+00 @@ -36,11 +36,11 @@ c, 4.4, 1.000000e+00 c, 5.5, 1.000000e+00 c, 6.6, 1.000000e+00 c, 7.7, 1.000000e+00 -p, O , 1.745149e+01, 3.818731e+00, 1.035449e+00, 2.602673e-01 +p, O , 1.745163e+01, 3.818766e+00, 1.035460e+00, 2.602755e-01 c, 1.1, 1.000000e+00 c, 2.2, 1.000000e+00 c, 3.3, 1.000000e+00 c, 4.4, 1.000000e+00 -d, O , 9.894508e-01 +d, O , 9.895363e-01 c, 1.1, 1.000000e+00 } From 2393d0a1452a04d5b3e8523ed720bfa1ee02b6e1 Mon Sep 17 00:00:00 2001 From: Grant Hill Date: Thu, 20 Apr 2023 10:42:36 +0100 Subject: [PATCH 02/11] Updates the multi-molecule tutorial documentation to reflect the code changes --- doc/src/_tutorials/multimol.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/src/_tutorials/multimol.rst b/doc/src/_tutorials/multimol.rst index c61676e..1e62fad 100644 --- a/doc/src/_tutorials/multimol.rst +++ b/doc/src/_tutorials/multimol.rst @@ -5,7 +5,7 @@ Multiple-molecule basis optimization ==================================== -This example demonstrates how BasisOpt can be used to optimize a double-zeta molecule-optimized basis set. In this case five molecules (water, methane, methanol, formaldehyde and oxygen) are used for the optimization, resulting in a single set of exponents for hydrogen, carbon and oxygen. Please note that as the exponents are tightly coupled this optimization can take a long time to run. The full example script can be found in ``examples/multi-molecule/multi-molecule.py``. +This example demonstrates how BasisOpt can be used to optimize a double-zeta molecule-optimized basis set. In this case five molecules (water, methane, methanol, formaldehyde and oxygen) are used for the optimization, resulting in a single set of exponents for hydrogen, carbon and oxygen. Please note that as the exponents are tightly coupled this optimization can take a long time to run. The full example script can be found in ``examples/multi-molecule/multi_molecule.py``. This example also shows the use of the logger functionality in BasisOpt. @@ -18,19 +18,19 @@ In this example we use the Psi4 program to carry out the electronic structure ca mb = MolecularBasis(name="double") list_of_mols = ['water', 'methane', 'methanol', 'formaldehyde', 'oxygen'] - mol_objs = [ - bo.molecule.Molecule.from_xyz(mol+'.xyz', name=mol) - for mol in list_of_mols - ] + mol_objs = [bo.molecule.Molecule.from_xyz(mol + '.xyz', name=mol) for mol in list_of_mols] mb = MolecularBasis(name="double", molecules=mol_objs) -We also set some calculation parameters that will be used in the optimization strategy. Specifically, we select the :math:`\omega` B97X-D density functional and turn off the use of density fitting in Psi4. +We also set some calculation parameters that will be used in the optimization strategy. Specifically, we select the :math:`\omega` B97X-D density functional, adjust the DFT integration grid, and turn off the use of density fitting in Psi4. .. code-block:: python params = { 'functional': "wb97x-d", - 'scf_type': "pk" + 'scf_type': "pk", + 'dft_spherical_points': "974", + 'dft_radial_points': "175", + 'dft_pruning_scheme': "none" } Optimization strategy and first run @@ -68,7 +68,7 @@ Within these iterations we also use the logging capability in BasisOpt to produc bo_logger.info("Starting consistency iteration %d", counter+1) mb.optimize() e_opt.append(strategy.last_objective) - e_diff = strategy.delta_objective + e_diff = abs(strategy.last_objective - e_opt[counter]) bo_logger.info("Objective function difference from previous iteration: %f\n", e_diff) counter += 1 From fbb77b497e0add6fad4a3dbd2b13a14120c6b591 Mon Sep 17 00:00:00 2001 From: Grant Hill Date: Thu, 20 Apr 2023 15:58:15 +0100 Subject: [PATCH 03/11] Adds rudimentary support for Molpro via pymolpro --- basisopt/api.py | 12 +++++ basisopt/wrappers/molpro.py | 102 ++++++++++++++++++++++++++++++++++++ 2 files changed, 114 insertions(+) create mode 100644 basisopt/wrappers/molpro.py diff --git a/basisopt/api.py b/basisopt/api.py index 43b0af8..6598e2f 100644 --- a/basisopt/api.py +++ b/basisopt/api.py @@ -149,6 +149,18 @@ def orca(path: str): bo_logger.info("ORCA install dir at: %s", path) +@register_backend +def molpro(path: str): + """Tests pymolpro import and prepares to be used as calculation backend""" + try: + global _CURRENT_BACKEND + from basisopt.wrappers.molpro import MolproWrapper + + _CURRENT_BACKEND = MolproWrapper() + except ImportError: + bo_logger.error("Molpro backend (using pymolpro) not found!") + + def run_calculation( evaluate: str = 'energy', mol: Molecule = None, params: dict[Any, Any] = {} ) -> int: diff --git a/basisopt/wrappers/molpro.py b/basisopt/wrappers/molpro.py new file mode 100644 index 0000000..1b891f7 --- /dev/null +++ b/basisopt/wrappers/molpro.py @@ -0,0 +1,102 @@ +# Wrappers for Molpro functionality using pymolpro (https://github.com/molpro/pymolpro) +from pymolpro import Project + +from basisopt.bse_wrapper import internal_basis_converter +from basisopt.containers import InternalBasis +from basisopt.exceptions import FailedCalculation +from basisopt.molecule import Molecule +from basisopt.wrappers.wrapper import Wrapper, available + + +class MolproWrapper(Wrapper): + """Wrapper for Molpro using pymolpro""" + + def __init__(self): + super().__init__(name='Molpro') + self._method_strings = { + 'hf': ['energy'], + 'rhf': ['energy'], + 'uhf': ['energy'], + } + + def convert_molecule(self, m: Molecule) -> str: + """Convert an internal Molecule object + to a Molpro geometry section and set charge/multiplicity + """ + molstring = "geomtyp=xyz\n" + molstring += "geom={\n" + for i in range(m.natoms()): + molstring += m.get_line(i) + "\n" + molstring += "}\n" + molstring += f"set,charge={m.charge}\n" + spin = m.multiplicity - 1 + molstring += f"set,spin={spin}\n" + return molstring + + def _command_string(self, method: str, **params) -> str: + """Helper function to turn an internal method + name into a Molpro command line + """ + command = f"{method}" + return command + "\n" + + def _convert_basis(self, basis: InternalBasis) -> str: + """Converts an InternalBasis to the basis string for Molpro + May be updated in future to enable auxiliary fitting sets + + Arguments: + basis (InternalBasis): basis set to convert + + Returns: + Molpro basis block string + """ + molpro_basis = internal_basis_converter(basis, fmt="molpro").split("\n") + basis_str = "" + for line in molpro_basis[1:-1]: + basis_str += line + "\n" + return basis_str + + def initialise(self, m: Molecule, name: str = "", tmp: str = "", **params) -> Project: + """Initialises pymolpro before each calculation + - creates a pymolpro Project + - converts molecule + - sets options from globals + - converts basis set + """ + # Create a Project + proj_name = f"{m.name}-{m.method}-" + name + p = Project(proj_name, location=tmp) + + # Handle options, molecule, basis + # TODO - add params + cmd = self._command_string(m.method) + mol = self.convert_molecule(m) + basis = self._convert_basis(m.basis) + + # Assemble into an input string and pass to the Project + molpro_input = mol + basis + cmd + p.write_input(molpro_input) + return p + + # def _get_properties( + # self, mol: Molecule, name: str = "prop", properties: list[str] = [], tmp: str = "", **params + # ) -> dict[str, Any]: + # """Helper function to run the calculation and + # retrieve a property value other than energy from Molpro. + # """ + # self.initialise(mol, name=name, tmp: str = "", **params) + # p.run(wait=True) + # if p.errors(): + # raise FailedCalculation + + # Retrieve the results + + @available + def energy(self, mol, tmp="", **params): + p = self.initialise(mol, name="energy", tmp=tmp, **params) + p.run(wait=True) + if p.errors(): + raise FailedCalculation + energy = p.energy() + p.clean() + return energy From a07951176d2906e57e1f9295e101471286b3cf9f Mon Sep 17 00:00:00 2001 From: Grant Hill Date: Thu, 20 Apr 2023 16:10:08 +0100 Subject: [PATCH 04/11] Adds the poetry lock file, may cause a clash later --- poetry.lock | 633 ++++++++++++++++++++++++---------------------------- 1 file changed, 296 insertions(+), 337 deletions(-) diff --git a/poetry.lock b/poetry.lock index 2d38604..bcba74a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. 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Hill Date: Thu, 20 Apr 2023 16:16:46 +0100 Subject: [PATCH 05/11] Forgot to run black on the multi molecule example --- examples/multi-molecule/multi_molecule.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/examples/multi-molecule/multi_molecule.py b/examples/multi-molecule/multi_molecule.py index 5664dc7..39c29fd 100644 --- a/examples/multi-molecule/multi_molecule.py +++ b/examples/multi-molecule/multi_molecule.py @@ -11,8 +11,13 @@ mol_objs = [bo.molecule.Molecule.from_xyz(mol + '.xyz', name=mol) for mol in list_of_mols] mb = MolecularBasis(name="double", molecules=mol_objs) -params = {'functional': "wb97x-d", 'scf_type': "pk", 'dft_spherical_points': "974", - 'dft_radial_points': "175", 'dft_pruning_scheme': "none"} +params = { + 'functional': "wb97x-d", + 'scf_type': "pk", + 'dft_spherical_points': "974", + 'dft_radial_points': "175", + 'dft_pruning_scheme': "none", +} strategy = Strategy() strategy.params = params From 1fae3ac40be46ad525671046a3772524c37c3163 Mon Sep 17 00:00:00 2001 From: Grant Hill Date: Wed, 26 Apr 2023 16:02:02 +0100 Subject: [PATCH 06/11] Adds MP2 and CC methods to the Molpro wrapper. Hopefully fixes occassional race condition problem. --- basisopt/wrappers/molpro.py | 41 +++++++++++++++++++++++++++++-------- 1 file changed, 32 insertions(+), 9 deletions(-) diff --git a/basisopt/wrappers/molpro.py b/basisopt/wrappers/molpro.py index 1b891f7..4037e56 100644 --- a/basisopt/wrappers/molpro.py +++ b/basisopt/wrappers/molpro.py @@ -17,6 +17,13 @@ def __init__(self): 'hf': ['energy'], 'rhf': ['energy'], 'uhf': ['energy'], + 'mp2': ['energy'], + 'rmp2': ['energy'], + 'ump2': ['energy'], + 'ccsd': ['energy'], + 'ccsd(t)': ['energy'], + 'uccsd': ['energy'], + 'uccsd(t)': ['energy'], } def convert_molecule(self, m: Molecule) -> str: @@ -37,7 +44,19 @@ def _command_string(self, method: str, **params) -> str: """Helper function to turn an internal method name into a Molpro command line """ - command = f"{method}" + # Post-HF calculations need to specify the HF part too + if method == "mp2": + command = "hf\nmp2" + elif method == "rmp2": + command = "rhf\nrmp2" + elif method == "ump2": + command = "uhf\nump2" + elif method[0:2] == "cc": + command = f"hf\n{method}" + elif method[0:3] == "ucc": + command = f"rhf\n{method}" + else: + command = f"{method}" return command + "\n" def _convert_basis(self, basis: InternalBasis) -> str: @@ -56,16 +75,13 @@ def _convert_basis(self, basis: InternalBasis) -> str: basis_str += line + "\n" return basis_str - def initialise(self, m: Molecule, name: str = "", tmp: str = "", **params) -> Project: + def initialise(self, proj: Project, m: Molecule, tmp: str = "", **params): """Initialises pymolpro before each calculation - creates a pymolpro Project - converts molecule - sets options from globals - converts basis set """ - # Create a Project - proj_name = f"{m.name}-{m.method}-" + name - p = Project(proj_name, location=tmp) # Handle options, molecule, basis # TODO - add params @@ -75,8 +91,7 @@ def initialise(self, m: Molecule, name: str = "", tmp: str = "", **params) -> Pr # Assemble into an input string and pass to the Project molpro_input = mol + basis + cmd - p.write_input(molpro_input) - return p + proj.write_input(molpro_input) # def _get_properties( # self, mol: Molecule, name: str = "prop", properties: list[str] = [], tmp: str = "", **params @@ -93,10 +108,18 @@ def initialise(self, m: Molecule, name: str = "", tmp: str = "", **params) -> Pr @available def energy(self, mol, tmp="", **params): - p = self.initialise(mol, name="energy", tmp=tmp, **params) + name = "energy" + proj_name = f"{mol.name}-{mol.method}-" + name + p = Project(proj_name, location=tmp) + self.initialise(p, mol, tmp=tmp, **params) p.run(wait=True) if p.errors(): raise FailedCalculation - energy = p.energy() + # TODO attempt to catch race cases where wait=True doesn't seem to be working + p.wait() + if mol.method == "hf": + energy = p.energy() + else: + energy = p.energy(method=f"{mol.method.upper()}") p.clean() return energy From 54eb398e8af0b15508e55896364dcd9f990ca1d3 Mon Sep 17 00:00:00 2001 From: Grant Hill Date: Thu, 27 Apr 2023 15:20:35 +0100 Subject: [PATCH 07/11] Adds rks and uks to energy methods and allows Molpro directives and options to be passed as parameters --- basisopt/wrappers/molpro.py | 48 ++++++++++++++++++++++++++----------- 1 file changed, 34 insertions(+), 14 deletions(-) diff --git a/basisopt/wrappers/molpro.py b/basisopt/wrappers/molpro.py index 4037e56..425c85c 100644 --- a/basisopt/wrappers/molpro.py +++ b/basisopt/wrappers/molpro.py @@ -24,6 +24,8 @@ def __init__(self): 'ccsd(t)': ['energy'], 'uccsd': ['energy'], 'uccsd(t)': ['energy'], + 'rks': ['energy'], + 'uks': ['energy'], } def convert_molecule(self, m: Molecule) -> str: @@ -40,23 +42,42 @@ def convert_molecule(self, m: Molecule) -> str: molstring += f"set,spin={spin}\n" return molstring + def _convert_params(self, method: str, **params) -> str: + """Helper function to pluck out the relevant + parameters for a given method. + Returns an empty string if the params are not found. + """ + method_search = method + '-params' + param_options = params.get(method_search, '') + return param_options + def _command_string(self, method: str, **params) -> str: """Helper function to turn an internal method name into a Molpro command line """ + # Extract the relevant parameters for this method + method_options = self._convert_params(method, **params) # Post-HF calculations need to specify the HF part too - if method == "mp2": - command = "hf\nmp2" - elif method == "rmp2": - command = "rhf\nrmp2" - elif method == "ump2": - command = "uhf\nump2" - elif method[0:2] == "cc": - command = f"hf\n{method}" - elif method[0:3] == "ucc": - command = f"rhf\n{method}" + # hence check for any user-supplied params for the HF part. + if method in ['mp2', 'ccsd', 'ccsd(t)']: + ref_options = self._convert_params('hf', **params) + command = f"{{hf{ref_options}}}\n{{{method}{method_options}}}" + elif method in ['rmp2', 'uccsd', 'uccsd(t)']: + ref_options = self._convert_params('rhf', **params) + command = f"{{rhf{ref_options}}}\n{{{method}{method_options}}}" + elif method in ['ump2']: + ref_options = self._convert_params('uhf', **params) + command = f"{{uhf{ref_options}}}\n{{{method}{method_options}}}" + # For DFT based methods, the functional must be specified separately + # to other params + elif method in ['rks', 'uks']: + if "functional" in params: + xcfun = params["functional"] + command = f"{{{method},{xcfun}{method_options}}}" + else: + raise KeyError("DFT functional not specified") else: - command = f"{method}" + command = f"{{{method}{method_options}}}" return command + "\n" def _convert_basis(self, basis: InternalBasis) -> str: @@ -84,8 +105,7 @@ def initialise(self, proj: Project, m: Molecule, tmp: str = "", **params): """ # Handle options, molecule, basis - # TODO - add params - cmd = self._command_string(m.method) + cmd = self._command_string(m.method, **params) mol = self.convert_molecule(m) basis = self._convert_basis(m.basis) @@ -115,7 +135,7 @@ def energy(self, mol, tmp="", **params): p.run(wait=True) if p.errors(): raise FailedCalculation - # TODO attempt to catch race cases where wait=True doesn't seem to be working + # Attempt to catch race cases where wait=True doesn't seem to be sufficient p.wait() if mol.method == "hf": energy = p.energy() From df0d2646ddcbaf4de8e3f4550ce7ad27310bdcc0 Mon Sep 17 00:00:00 2001 From: Grant Hill Date: Mon, 8 May 2023 12:06:37 +0100 Subject: [PATCH 08/11] Adds a helper function to the Molpro wrapper to retrieve energies --- basisopt/wrappers/molpro.py | 36 ++++++++++++++++++++---------------- 1 file changed, 20 insertions(+), 16 deletions(-) diff --git a/basisopt/wrappers/molpro.py b/basisopt/wrappers/molpro.py index 425c85c..d3de934 100644 --- a/basisopt/wrappers/molpro.py +++ b/basisopt/wrappers/molpro.py @@ -113,18 +113,20 @@ def initialise(self, proj: Project, m: Molecule, tmp: str = "", **params): molpro_input = mol + basis + cmd proj.write_input(molpro_input) - # def _get_properties( - # self, mol: Molecule, name: str = "prop", properties: list[str] = [], tmp: str = "", **params - # ) -> dict[str, Any]: - # """Helper function to run the calculation and - # retrieve a property value other than energy from Molpro. - # """ - # self.initialise(mol, name=name, tmp: str = "", **params) - # p.run(wait=True) - # if p.errors(): - # raise FailedCalculation - - # Retrieve the results + def _get_energy(self, proj: Project, meth: str) -> float: + """Helper function to retrieve the energy from + Molpro after a calculation""" + if meth in ['hf', 'rhf', 'uhf', 'rks', 'uks']: + energy = proj.energies()[0] + elif meth in ['mp2']: + energy = proj.energies()[-1] + elif meth in ['rmp2', 'ump2', 'ccsd']: + energy = proj.energies(method=f"{meth.upper()}")[-1] + elif meth in ['uccsd', 'uccsd(t)']: + energy = proj.energy(method=f"RHF-{meth.upper()}") + else: + energy = proj.energy(method=f"{meth.upper()}") + return energy @available def energy(self, mol, tmp="", **params): @@ -137,9 +139,11 @@ def energy(self, mol, tmp="", **params): raise FailedCalculation # Attempt to catch race cases where wait=True doesn't seem to be sufficient p.wait() - if mol.method == "hf": - energy = p.energy() - else: - energy = p.energy(method=f"{mol.method.upper()}") + # TODO use a helper function to extract the energy for a particular method + energy = self._get_energy(p, mol.method) + # if mol.method == "hf": + # energy = p.energy() + # else: + # energy = p.energy(method=f"{mol.method.upper()}") p.clean() return energy From 2b49ac57f996509d20a06e33d010bffa0c5510cc Mon Sep 17 00:00:00 2001 From: Grant Hill Date: Fri, 12 May 2023 11:04:53 +0100 Subject: [PATCH 09/11] Documentation/guide to using the Molpro wrapper. Not currently linked from elsewhere in the docs. --- doc/src/molpro.rst | 70 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 doc/src/molpro.rst diff --git a/doc/src/molpro.rst b/doc/src/molpro.rst new file mode 100644 index 0000000..69fb887 --- /dev/null +++ b/doc/src/molpro.rst @@ -0,0 +1,70 @@ +.. basisopt molpro wrapper file + +.. _`sec:molpro`: + +========================= +Using Molpro as a backend +========================= + +The Molpro backend for BasisOpt uses the pymolpro Python library. Both the commercial +`Molpro quantum chemistry package `_ and the free `pymolpro library `_ +must be available to use the backend. The backend can then specified in the same manner as for other quantum chemistry packages. + +.. code-block:: python + + bo.set_backend('molpro') + bo.set_tmp_dir('/tmp/') + +This guide is intended to highlight how to specify certain types of Molpro calculation via BasisOpt, including passing Molpro options and +directives. + +Density Functional Theory calculations +====================================== + +In Molpro, Kohn-Sham DFT calculations are requested using either the ``rks`` or ``uks`` commands, for spin-restricted and spin-unrestricted, respectively. The exchange-correlation functional must also be specified. To maintain consistency with other BasisOpt backends, the choice of +functional is specified by setting the ``functional`` params. For example, a PBE0 calculation using the spin-restricted Kohn-Sham program +can be setup as: + +.. code-block:: python + + params = {'functional': "pbe0"} + strategy = Strategy() + mb.setup(method='rks', strategy=strategy, params=params) + +Specifying options and directives +================================= + +A `params` block is used to pass options and directives to Molpro on a per-method basis. This is done using a *method*-params key and, as +an example, requesting that no orbitals are treated with a frozen-core approximation in an MP2 calculation can be specified in the +following way: + +.. code-block:: python + + params = {'mp2-params': ";core,0"} + strategy = Strategy() + mb.setup(method='mp2', strategy=strategy, params=params) + +Note that the ``;`` and ``,`` separators used in Molpro input files must be included as part of the params values. + +Post-HF methods +=============== + +When running a post-Hartree-Fock calculation in Molpro, the reference wavefunction must also be specified. In BasisOpt, the reference +calculation is somewhat *hard-coded* and will be determined from the post-HF method selected. Currently, requesting a method of `mp2`, +`ccsd` or `ccsd(t)` will use a `hf` reference. The methods `rmp2`, `uccsd` and `uccsd(t)` will use an `rhf` reference, and `ump2` uses +the spin-unrestricted `uhf` reference. + +It is possible to pass Molpro options and/or directives to both the reference and the correlated calculation. For example, to increase +the accuracy of the HF reference and also request that no orbitals are treated with a frozen-core approximation in an MP2 calculation: + +.. code-block:: python + + params = {'hf-params': ";accu,14", 'mp2-params': ";core,0"} + strategy = Strategy() + mb.setup(method='mp2', strategy=strategy, params=params) + +Parameters for an RHF reference would use an ``rhf-params`` key, while a UHF reference would require ``uhf-params``. + + +.. toctree:: + :hidden: From bd5825733c6a1866298c7a373c2ca2e0c98c9114 Mon Sep 17 00:00:00 2001 From: Grant Hill Date: Fri, 19 May 2023 16:03:56 +0100 Subject: [PATCH 10/11] Enables use of Molpro globals --- basisopt/wrappers/molpro.py | 7 ++++++- doc/src/molpro.rst | 10 ++++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/basisopt/wrappers/molpro.py b/basisopt/wrappers/molpro.py index d3de934..f35cd45 100644 --- a/basisopt/wrappers/molpro.py +++ b/basisopt/wrappers/molpro.py @@ -105,12 +105,17 @@ def initialise(self, proj: Project, m: Molecule, tmp: str = "", **params): """ # Handle options, molecule, basis + g_param_str = "" + glo_params = params.get("global-params", '') + if glo_params: + g_param_str = glo_params + "\n" cmd = self._command_string(m.method, **params) mol = self.convert_molecule(m) basis = self._convert_basis(m.basis) # Assemble into an input string and pass to the Project - molpro_input = mol + basis + cmd + molpro_input = g_param_str + mol + basis + cmd + print(molpro_input) proj.write_input(molpro_input) def _get_energy(self, proj: Project, meth: str) -> float: diff --git a/doc/src/molpro.rst b/doc/src/molpro.rst index 69fb887..b72a623 100644 --- a/doc/src/molpro.rst +++ b/doc/src/molpro.rst @@ -46,6 +46,16 @@ following way: Note that the ``;`` and ``,`` separators used in Molpro input files must be included as part of the params values. +Specifying global parameters and thresholds +=========================================== + +Molpro global parameters and thresholds are also specified in the params dictionary, using the global-params key. For example, +to set a global energy convergence threshold: + +.. code-block:: python + + params = {'global-params': "gthresh,energy=1.d-12"} + Post-HF methods =============== From ef412ed994ade48ba4d91f337b60ecd3282c5860 Mon Sep 17 00:00:00 2001 From: Robert Shaw Date: Fri, 27 Jun 2025 01:39:31 +0100 Subject: [PATCH 11/11] Restored previous poetry lock --- poetry.lock | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/poetry.lock b/poetry.lock index bcba74a..4dbf6a6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. [[package]] name = "alabaster"