From 0e70ec235c4b2af707406923fc2a8923ed98967d Mon Sep 17 00:00:00 2001 From: Michele Ceriotti Date: Tue, 12 Nov 2024 22:04:41 +0100 Subject: [PATCH] A "direct" FF using the same PES interfaces as the python driver (#390) This is a major restructuring of the python driver and the forcefield block. All PES drivers have been moved to an ipi/pes folder, and their API streamlined with the possibility of providing both lists of arguments and named arguments. A new FFDirect forcefield makes it possible to call the PES from i-PI directly, avoiding the client/server setup that many find confusing. We converted most PES to the new interfaces, but several are possibly broken; these now trigger a warning so that users can check and possibly fix them. --------- Co-authored-by: Yair Litman Co-authored-by: Venkat Kapil --- docs/scripts/help.py | 1 + docs/src/contributing.rst | 8 +- docs/src/getting-started.rst | 26 +- docs/src/index.rst | 4 +- drivers/py/driver.py | 27 +- drivers/py/pes/mace.py | 40 -- drivers/py/pes/metatensor.py | 94 ----- drivers/py/pes/so3lr.py | 42 -- examples/clients/mace/RESTART | 365 ++++++++++++++++++ examples/clients/mace/getmodel.sh | 3 + examples/clients/mace/init.xyz | 1 + examples/clients/mace/input.xml | 37 ++ examples/clients/metatensor/README.md | 14 +- examples/clients/metatensor/create-model.py | 4 +- examples/clients/metatensor/input-direct.xml | 47 +++ examples/clients/metatensor/nickel-lj.pt | Bin 30459 -> 37924 bytes examples/clients/pes/README.md | 8 + examples/clients/pes/harmonic-direct/Makefile | 17 + examples/clients/pes/harmonic-direct/init.xyz | 3 + .../clients/pes/harmonic-direct/input.xml | 38 ++ .../pes/harmonic-direct/test_settings.dat | 0 examples/clients/xtb/config.json | 1 + examples/clients/xtb/run.sh | 2 +- .../implicit_bath_pos-dependent/run.sh | 9 +- examples/init_files/water_64mols.extxyz | 194 ++++++++++ ipi/__init__.py | 1 + ipi/engine/forcefields.py | 89 ++++- ipi/inputs/forcefields.py | 61 ++- ipi/inputs/simulation.py | 31 +- {drivers/py => ipi}/pes/__init__.py | 0 {drivers/py => ipi}/pes/ase.py | 51 ++- {drivers/py => ipi}/pes/bath.py | 27 +- {drivers/py => ipi}/pes/doubledoublewell.py | 66 ++-- {drivers/py => ipi}/pes/doublewell.py | 26 +- .../py => ipi}/pes/doublewell_with_bath.py | 57 +-- .../pes/doublewell_with_friction.py | 59 +-- {drivers/py => ipi}/pes/driverdipole.py | 24 +- {drivers/py => ipi}/pes/dummy.py | 21 +- {drivers/py => ipi}/pes/elphmod.py | 23 +- {drivers/py => ipi}/pes/harmonic.py | 36 +- ipi/pes/mace.py | 53 +++ ipi/pes/metatensor.py | 98 +++++ {drivers/py => ipi}/pes/pet.py | 91 ++--- {drivers/py => ipi}/pes/rascal.py | 52 +-- ipi/pes/so3lr.py | 37 ++ {drivers/py => ipi}/pes/spline.py | 20 +- {drivers/py => ipi}/pes/xtb.py | 48 +-- ipi/utils/io/inputs/__init__.py | 34 ++ ipi/utils/io/inputs/io_xml.py | 3 +- ipi_tests/README.md | 5 +- .../profiling/classical_md_direct/init.xyz | 10 + .../profiling/classical_md_direct/input.xml | 34 ++ ipi_tests/profiling/run_profiling.sh | 2 +- .../simulation.instanton_FINAL_15.ener | 33 -- .../100K_implicit_friction/test_settings.dat | 2 +- setup.py | 9 +- 56 files changed, 1533 insertions(+), 555 deletions(-) delete mode 100644 drivers/py/pes/mace.py delete mode 100644 drivers/py/pes/metatensor.py delete mode 100644 drivers/py/pes/so3lr.py create mode 100644 examples/clients/mace/RESTART create mode 100644 examples/clients/mace/getmodel.sh create mode 120000 examples/clients/mace/init.xyz create mode 100644 examples/clients/mace/input.xml create mode 100644 examples/clients/metatensor/input-direct.xml create mode 100644 examples/clients/pes/README.md create mode 100644 examples/clients/pes/harmonic-direct/Makefile create mode 100644 examples/clients/pes/harmonic-direct/init.xyz create mode 100644 examples/clients/pes/harmonic-direct/input.xml create mode 100644 examples/clients/pes/harmonic-direct/test_settings.dat create mode 100644 examples/clients/xtb/config.json create mode 100644 examples/init_files/water_64mols.extxyz rename {drivers/py => ipi}/pes/__init__.py (100%) rename {drivers/py => ipi}/pes/ase.py (70%) rename {drivers/py => ipi}/pes/bath.py (79%) rename {drivers/py => ipi}/pes/doubledoublewell.py (71%) rename {drivers/py => ipi}/pes/doublewell.py (73%) rename {drivers/py => ipi}/pes/doublewell_with_bath.py (65%) rename {drivers/py => ipi}/pes/doublewell_with_friction.py (71%) rename {drivers/py => ipi}/pes/driverdipole.py (95%) rename {drivers/py => ipi}/pes/dummy.py (71%) rename {drivers/py => ipi}/pes/elphmod.py (55%) rename {drivers/py => ipi}/pes/harmonic.py (60%) create mode 100644 ipi/pes/mace.py create mode 100644 ipi/pes/metatensor.py rename {drivers/py => ipi}/pes/pet.py (53%) rename {drivers/py => ipi}/pes/rascal.py (56%) create mode 100644 ipi/pes/so3lr.py rename {drivers/py => ipi}/pes/spline.py (84%) rename {drivers/py => ipi}/pes/xtb.py (74%) create mode 100644 ipi_tests/profiling/classical_md_direct/init.xyz create mode 100644 ipi_tests/profiling/classical_md_direct/input.xml delete mode 100644 ipi_tests/regression_tests/tests/INSTANTON/100K_implicit_friction/simulation.instanton_FINAL_15.ener diff --git a/docs/scripts/help.py b/docs/scripts/help.py index 541281e7e..3c646b862 100644 --- a/docs/scripts/help.py +++ b/docs/scripts/help.py @@ -87,6 +87,7 @@ "h0": cell.InputCell(), "forcefield": forcefields.InputForceField(), "ffsocket": forcefields.InputFFSocket(), + "ffdirect": forcefields.InputFFDirect(), "fflj": forcefields.InputFFLennardJones(), "ffdebye": forcefields.InputFFDebye(), "ffplumed": forcefields.InputFFPlumed(), diff --git a/docs/src/contributing.rst b/docs/src/contributing.rst index 7b2a9313d..32955b51c 100644 --- a/docs/src/contributing.rst +++ b/docs/src/contributing.rst @@ -1,3 +1,5 @@ +.. _contributing: + Contributing ============ @@ -89,7 +91,11 @@ If your new development in i-PI is directly related to a specific client code or We very much welcome new interfaces and we will be happy to answer your questions. If you want to enable the communication of a new client code with i-PI, it is not difficult: Please check an example of how it was done in ``fortran`` and ``python`` in the `drivers` folder in the repository. - +It is especially simple to add a new potential energy that is evaluated in Python: it is sufficient to add a file in the `ipi/pes` folder, specifying +`__DRIVER_NAME__` (a string that will be used to refer to the PES from the i-PI input or the command line) and `__DRIVER_CLASS__`, the name of the +actual class, that should provide, directly or through inheritance, a `__call__(self, cell, pos)` function and return a tuple with +`(potential, forces, virial, extras)`. See any of the existing PES files to use as templates - it is particularly simple to create a class that +piggybacs on an existing ASE-style calculator. Getting recognition for your contribution diff --git a/docs/src/getting-started.rst b/docs/src/getting-started.rst index fcc32010e..0d8c176ff 100644 --- a/docs/src/getting-started.rst +++ b/docs/src/getting-started.rst @@ -83,9 +83,29 @@ The built-in driver requires a FORTRAN compiler, and can be built as make cd ../.. +Python driver and PES +^^^^^^^^^^^^^^^^^^^^^ + +In addition to the FORTRAN drive, the i-PI distribution contains also a Python +driver, available in `drivers/py` and through the command-line command +`i-pi-py_driver`, which evaluates potential energy surfaces evaluated by simple +driver classes, that can be found in `ipi/pes`. + +These classes are particularly suitable to perform inference with machine-learning +potentials implemented in Python, and it is reasonably simple to add your own, +if you need to (see also the :ref:`contributing` section). + +These PES files can also be used directly, without the need to go through a +client-server interface, using a :ref:`ffdirect` forcefield, including in the +XML input a block similar to + +.. code-block:: + + + harmonic + { k1: 1.0} + -There is also a Python driver available in `drivers/py`, which however has limited -functionalities. Alternative installation using the setup.py module ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -266,7 +286,7 @@ The flags do the following: -S: Optional parameter. If given, overwrite the default socket prefix used in the creation of files for the socket communication. - (default "/tmp/ipi_") + (default "/tmp/ipi\_") This code should be fairly simple to extend to other pair-wise interaction potentials, and examples of its use can be seen in the diff --git a/docs/src/index.rst b/docs/src/index.rst index 37b4c4f72..a0eeb385d 100644 --- a/docs/src/index.rst +++ b/docs/src/index.rst @@ -26,9 +26,8 @@ This documentation is structured as follows: :maxdepth: 2 introduction - onlinereso - features getting-started + features units input-files input-tags @@ -36,6 +35,7 @@ This documentation is structured as follows: output-tags distributed tutorials + onlinereso faq troubleshooting contributing diff --git a/drivers/py/driver.py b/drivers/py/driver.py index aeff7f8e4..98cab93f4 100755 --- a/drivers/py/driver.py +++ b/drivers/py/driver.py @@ -3,12 +3,8 @@ import argparse import numpy as np - -try: - from pes import * -except ImportError: - # when in an installed i-PI package - from ipi._driver.pes import * +from ipi.pes import * +from ipi.utils.io.inputs import read_args_kwargs description = """ Minimal example of a Python driver connecting to i-PI and exchanging energy, forces, etc. @@ -205,8 +201,8 @@ def run_driver( "--mode", type=str, default="dummy", + choices=list(__drivers__.keys()), help="""Type of potential to be used to compute the potential and its derivatives. - Currently implemented: [dummy, harmonic] """, ) parser.add_argument( @@ -227,10 +223,23 @@ def run_driver( args = parser.parse_args() + driver_args, driver_kwargs = read_args_kwargs(args.param) + if args.mode in __drivers__: - d_f = __drivers__[args.mode](args.param, args.verbose) + try: + d_f = __drivers__[args.mode]( + *driver_args, verbose=args.verbose, **driver_kwargs + ) + except ImportError: + # specific errors have already been triggered + raise + except Exception as err: + print(f"Error setting up PES mode {args.mode}") + print(__drivers__[args.mode].__doc__) + print("Error trace: ") + raise err elif args.mode == "dummy": - d_f = Dummy_driver(args.param, args.verbose) + d_f = Dummy_driver(verbose=args.verbose) else: raise ValueError("Unsupported driver mode ", args.mode) diff --git a/drivers/py/pes/mace.py b/drivers/py/pes/mace.py deleted file mode 100644 index 881f9e5cd..000000000 --- a/drivers/py/pes/mace.py +++ /dev/null @@ -1,40 +0,0 @@ -""" An interface for the [MACE](https://github.com/ACEsuit/mace) calculator """ - -import sys -from .ase import ASEDriver - -try: - from mace.calculators import MACECalculator -except: - MACECalculator = None - -__DRIVER_NAME__ = "mace" -__DRIVER_CLASS__ = "MACE_driver" - -ERROR_MSG = """ -MACE driver requires specification of a .json model, -and a template file that describes the chemical makeup of the structure. - -Example: python driver.py -m mace -u -o model.json,template.xyz -""" - - -class MACE_driver(ASEDriver): - def __init__(self, args=None, verbose=False): - if MACECalculator is None: - raise ImportError("Couldn't load mace bindings") - - super().__init__(args, verbose, ERROR_MSG) - - def check_arguments(self): - """Check the arguments requuired to run the driver - - This loads the potential and atoms template in MACE - """ - - super().check_arguments() - - if len(self.args) < 2: - sys.exit(self.error_msg) - - self.ase_calculator = MACECalculator(model_paths=self.args[1], device="cpu") diff --git a/drivers/py/pes/metatensor.py b/drivers/py/pes/metatensor.py deleted file mode 100644 index 271a0c04e..000000000 --- a/drivers/py/pes/metatensor.py +++ /dev/null @@ -1,94 +0,0 @@ -""" -Interface with metatensor -(https://lab-cosmo.github.io/metatensor/latest/atomistic/index.html), that can -be used to perform calculations based on different types of machine learning -potentials -""" - -import sys - -from ipi.utils.messages import warning - -from .ase import ASEDriver - -try: - import metatensor.torch - from metatensor.torch.atomistic.ase_calculator import MetatensorCalculator -except ImportError as e: - warning(f"Could not find or import metatensor.torch: {e}") - MetatensorCalculator = None - -__DRIVER_NAME__ = "metatensor" -__DRIVER_CLASS__ = "MetatensorDriver" - -ERROR_MSG = """ -The metatensor driver requires specification of a .pt TorchScript model and an -ASE-readable template file that describes the chemical makeup of the structure. - -Example: python driver.py -m metatensor -u -o template.xyz,model.pt,device=cpu,\ -extensions=path/to/extensions,check_consistency=False -""" - - -class MetatensorDriver(ASEDriver): - def __init__(self, args=None, verbose=False, error_msg=ERROR_MSG): - super().__init__(args, verbose, error_msg) - - def check_arguments(self): - """Check the arguments required to run the driver - - This loads the potential and atoms template in metatensor - """ - - if MetatensorCalculator is None: - raise ImportError("could not import metatensor.torch, is it installed?") - - metatensor_major, metatensor_minor, *_ = metatensor.torch.__version__.split(".") - metatensor_major = int(metatensor_major) - metatensor_minor = int(metatensor_minor) - - if metatensor_major != 0 or metatensor_minor != 5: - raise ImportError( - "this code is only compatible with metatensor-torch v0.5.x, " - f"found version v{metatensor.torch.__version__} " - f"at '{metatensor.torch.__file__}'" - ) - - super().check_arguments() - - if len(self.args) < 2: - sys.exit(self.error_msg) - self.model_path = self.args[1] - - device = None - extensions_directory = None - check_consistency = False - for arg in self.args[2:]: - if arg.startswith("device="): - device = arg[7:] - elif arg.startswith("extensions="): - extensions_directory = arg[11:] - elif arg.startswith("check_consistency="): - arg = arg[18:] - if arg == "True": - check_consistency = True - elif arg == "False": - check_consistency = False - else: - raise ValueError( - "invalid value for check_consistency, expected True or False, " - f"got {arg}" - ) - - else: - sys.exit(self.error_msg) - - self.ase_calculator = MetatensorCalculator( - self.model_path, - device=device, - extensions_directory=extensions_directory, - check_consistency=check_consistency, - ) - - # Show the model metadata to the users - print(self.ase_calculator.metadata()) diff --git a/drivers/py/pes/so3lr.py b/drivers/py/pes/so3lr.py deleted file mode 100644 index ee9599684..000000000 --- a/drivers/py/pes/so3lr.py +++ /dev/null @@ -1,42 +0,0 @@ -""" An interface for the [SO3LR](https://github.com/general-molecular-simulations/so3lr) calculator """ - -from .ase import ASEDriver - -try: - from so3lr import So3lrCalculator -except: - So3lrCalculator = None - -__DRIVER_NAME__ = "so3lr" -__DRIVER_CLASS__ = "SO3LR_driver" - -ERROR_MSG = """ -SO3LR driver requires a template file that describes the chemical makeup of the structure. - -Optionally, lr_cutoff and dispersion_energy_lr_cutoff_damping can be specified. - -Example: python driver.py -m so3lr -u -o template.xyz,lr_cutoff=12,dispersion_energy_lr_cutoff_damping=2 -""" - - -class SO3LR_driver(ASEDriver): - def __init__(self, args=None, verbose=False): - if So3lrCalculator is None: - raise ImportError("Couldn't load so3lr bindings") - - super().__init__(args, verbose, ERROR_MSG) - - def check_arguments(self): - super().check_arguments() - - args = self.args - - kwargs = {} - if len(args) >= 2: - _ = args[0] # template we don't need - - for arg in args[1:]: - key, value = arg.split("=") - kwargs[key] = float(value) - - self.ase_calculator = So3lrCalculator(**kwargs) diff --git a/examples/clients/mace/RESTART b/examples/clients/mace/RESTART new file mode 100644 index 000000000..3be060e83 --- /dev/null +++ b/examples/clients/mace/RESTART @@ -0,0 +1,365 @@ + + + 31415 + [{"bit_generator": "MT19937", "state": {"key": [795669418, 3354365008, 150463171, 3937589838, 937846891, 734296723, 764622735, 1183299804, 1272117760, 2010368631, 1241689493, 3626464784, 1162653305, 1289276628, 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+ + [ 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, + 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, + 1.83747161e+03, 2.91643931e+04, 1.83747161e+03, 1.83747161e+03, 2.91643931e+04, + 1.83747161e+03, 1.83747161e+03 ] + + + [ O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H, O, H, H, + O, H, H, O, H, + H, O, H, H, O, + H, H ] + + + + [ 1.96756566e+01, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.96756566e+01, + 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 1.96756566e+01 ] + + + diff --git a/examples/clients/mace/getmodel.sh b/examples/clients/mace/getmodel.sh new file mode 100644 index 000000000..31ee1ca0d --- /dev/null +++ b/examples/clients/mace/getmodel.sh @@ -0,0 +1,3 @@ +wget wget https://github.com/ACEsuit/mace-mp/releases/download/mace_mp_0c/mace-small-density-agnesi-stress.model +mv mace-small-density-agnesi-stress.model mace.model + diff --git a/examples/clients/mace/init.xyz b/examples/clients/mace/init.xyz new file mode 120000 index 000000000..0db27c06d --- /dev/null +++ b/examples/clients/mace/init.xyz @@ -0,0 +1 @@ +../../init_files/water_64mols.extxyz \ No newline at end of file diff --git a/examples/clients/mace/input.xml b/examples/clients/mace/input.xml new file mode 100644 index 000000000..72103e52f --- /dev/null +++ b/examples/clients/mace/input.xml @@ -0,0 +1,37 @@ + + + + [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_md{electronvolt}, potential{electronvolt}, pressure_md{megapascal} ] + positions + + + 20000 + + 31415 + + +
driver
+ + + + init.xyz + 300 + + + + + + + + + 100 + + + 0.50 + + + + 300 + + + diff --git a/examples/clients/metatensor/README.md b/examples/clients/metatensor/README.md index a5b0f23c2..c36c2a1b0 100644 --- a/examples/clients/metatensor/README.md +++ b/examples/clients/metatensor/README.md @@ -10,14 +10,14 @@ machine learning potentials. ## Installation -The code is compatible with metatensor-torch v0.5, which you can install with +The code is compatible with metatensor-torch v0.6, which you can install with ```bash # install all metatensor packages simultaneously pip install "metatensor[torch]" # install packages individually, with explicit control over the installed versions -pip install "metatensor-torch ==0.5.*" "metatensor-operations ==0.2.*" +pip install "metatensor-torch ==0.6.*" "metatensor-operations ==0.2.*" ``` ## Running the example @@ -42,3 +42,13 @@ The options (after `-o`) are as follow: - `check_consistency` controls whether we should run some extra internal consistency checks about data given to the model and data returned by the model. + +## Running with FFDirect + +It is also possible to run the metatensor PES directly, without the need for an external +driver. To do so, you need to use a `` clause in the input, and specify +the appropriate options as a dictionary. Then, you can simply run + +```bash +i-pi input-direct.xml +``` diff --git a/examples/clients/metatensor/create-model.py b/examples/clients/metatensor/create-model.py index f821b73b2..9b442be83 100644 --- a/examples/clients/metatensor/create-model.py +++ b/examples/clients/metatensor/create-model.py @@ -13,7 +13,7 @@ with_extension=False, ) -model.export("nickel-lj.pt") +model.save("nickel-lj.pt") model = metatensor_lj_test.lennard_jones_model( @@ -25,4 +25,4 @@ energy_unit="kcal/mol", with_extension=True, ) -model.export("nickel-lj-extensions.pt", collect_extensions="collected-extensions/") +model.save("nickel-lj-extensions.pt", collect_extensions="collected-extensions/") diff --git a/examples/clients/metatensor/input-direct.xml b/examples/clients/metatensor/input-direct.xml new file mode 100644 index 000000000..9422cd787 --- /dev/null +++ b/examples/clients/metatensor/input-direct.xml @@ -0,0 +1,47 @@ + + + + [step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, + kinetic_md{electronvolt}, potential{electronvolt}, pressure_md{bar}, + volume{angstrom3}, ensemble_temperature{kelvin}, cell_abcABC] + + x_centroid{angstrom} + + + 1000 +12345 + + + metatensor + {template:nickel.xyz,model:nickel-lj.pt,device:cpu } + + + + + nickel.xyz + 250.0 + + + + + + + + 0.5 + + [ + 4.49e-3, 6.59e-6, 2.79e-4, -8.81e-4, 5.61e-3, + -6.73e-6, 2.08e-9, 1.75e-5, -4.80e-6, 1.03e-5, + -3.59e-4, -1.75e-5, 3.29e-5, 1.24e-4, -2.42e-4, + -2.51e-4, 4.80e-6, -1.24e-4, 6.45e-4, 2.78e-4, + 5.27e-3, -1.03e-5, 2.42e-4, -2.78e-4, 7.49e-3 + ] + + + + + + 250.0 + + + diff --git a/examples/clients/metatensor/nickel-lj.pt b/examples/clients/metatensor/nickel-lj.pt index 9491841ca0bd70e87d0c78be7152f2cf24a0c84a..c9765a0ebbe5dfbe319e8245b90dc8c662ebaca6 100644 GIT binary patch delta 29961 zcmZU)b8sd;)HZzAwrzWB+wRu3ZQpgbwz;)!ZEf4!t=+Bfw(tI)=bic9nJ<$`GMSTH zSMt|6Ial7Vz)C8>6Y(KP0OBbuU<66?Fkr$dKNU$*jKN5gzG|sS0Bit98#6l#dnS8Z z77K58SCfCOvy-bklY@o3iMffpiIf=Ae=Cx1QB?fM|4mqs^O2H&WBta##K!ios5ke3F 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file is part of i-PI. +# i-PI Copyright (C) 2014-2015 i-PI developers +# See the "licenses" directory for full license information. + +.PHONY: all clean harmonic +all: harmonic + +IPI:=i-pi + + +harmonic: + $(IPI) input.xml + +clean: + rm -f *simulation.* RESTART EXIT diff --git a/examples/clients/pes/harmonic-direct/init.xyz b/examples/clients/pes/harmonic-direct/init.xyz new file mode 100644 index 000000000..8efa9e7ef --- /dev/null +++ b/examples/clients/pes/harmonic-direct/init.xyz @@ -0,0 +1,3 @@ +1 + +H 0.108 0.000 0.000 diff --git a/examples/clients/pes/harmonic-direct/input.xml b/examples/clients/pes/harmonic-direct/input.xml new file mode 100644 index 000000000..b3b5ba4b6 --- /dev/null +++ b/examples/clients/pes/harmonic-direct/input.xml @@ -0,0 +1,38 @@ + + + [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin}, potential{kelvin}, pressure_cv{megapascal}] + positions{angstrom} + forces{piconewton} + + 100 + + 3348 + + + harmonic + { k1:1.0 } + + + + + [ 15., 15.0, 15.0 ] + + init.xyz + 3683.412077 + + + + + + 3683.412077 + + + + + 25 + + 0.003 + + + + diff --git a/examples/clients/pes/harmonic-direct/test_settings.dat b/examples/clients/pes/harmonic-direct/test_settings.dat new file mode 100644 index 000000000..e69de29bb diff --git a/examples/clients/xtb/config.json b/examples/clients/xtb/config.json new file mode 100644 index 000000000..f299cd2e4 --- /dev/null +++ b/examples/clients/xtb/config.json @@ -0,0 +1 @@ +{"method": "GFN2-xTB", "numbers": [6,1,1,1,1], "periodic": false} diff --git a/examples/clients/xtb/run.sh b/examples/clients/xtb/run.sh index 3726ce141..98eea7e55 100644 --- a/examples/clients/xtb/run.sh +++ b/examples/clients/xtb/run.sh @@ -3,5 +3,5 @@ echo "Running i-PI" i-pi input.xml &> log.ipi & sleep 1 echo "Running driver" -i-pi-py_driver -m xtb -o '{"method": "GFN2-xTB", "numbers": [6,1,1,1,1], "periodic": false}' -u -a xtb &> log.xtb +i-pi-py_driver -m xtb -o config.json -u -a xtb &> log.xtb diff --git a/examples/features/ring_polymer_instanton/rates_1D_double_well_with_friction/implicit_bath_pos-dependent/run.sh b/examples/features/ring_polymer_instanton/rates_1D_double_well_with_friction/implicit_bath_pos-dependent/run.sh index 8bc25bc1e..3ee1793d9 100755 --- a/examples/features/ring_polymer_instanton/rates_1D_double_well_with_friction/implicit_bath_pos-dependent/run.sh +++ b/examples/features/ring_polymer_instanton/rates_1D_double_well_with_friction/implicit_bath_pos-dependent/run.sh @@ -5,9 +5,9 @@ wc=500 V0=2085 mass=1837.36223469 - x0=0 epsilon=-1.0 delta=0 + epsilon2=0 deltaQ=1 address=localhost @@ -19,4 +19,9 @@ sleep 3 #Launch driver - i-pi-driver-py -m ${model} -o ${wb},${V0},${mass},${x0},${eta},${epsilon},${delta},${deltaQ} -u -a ${address} + #i-pi-driver-py -m ${model} -o ${wb},${V0},${mass},${x0},${eta},${epsilon},${delta},${deltaQ} -u -a ${address} + arg="w_b=${wb},v0=${V0},m=${mass},delta=${delta},eta0=${eta},eps1=${epsilon},eps2=${epsilon2},deltaQ=${deltaQ}" + + echo ${arg} +# def __init__(self,w_b=None,v0=None,m=None,eta0=None,eps1=None,eps2=None,delta=None,deltaQ=None, *args, **kwargs): + i-pi-driver-py -m ${model} -o ${arg} -u -a ${address} diff --git a/examples/init_files/water_64mols.extxyz b/examples/init_files/water_64mols.extxyz new file mode 100644 index 000000000..7e35fe97f --- /dev/null +++ b/examples/init_files/water_64mols.extxyz @@ -0,0 +1,194 @@ +192 +Lattice="10.4119090601988 0 0 0 10.4119090601988 0 0 0 10.4119090601988" +O 11.18136 -7.24116 6.42199 +H 11.31672 -7.89411 5.71998 +H 11.94205 -7.06097 7.01033 +O 2.78582 1.60883 1.56485 +H 2.45814 1.98676 2.52844 +H 3.72449 1.60021 1.79886 +O 4.06425 1.21834 6.13650 +H 4.52259 0.84151 5.38020 +H 3.73582 0.62974 6.86168 +O -5.85212 -1.78980 -1.47238 +H -5.90795 -2.64483 -2.11048 +H -6.81342 -1.58626 -1.68821 +O -0.69190 1.48298 4.64653 +H -0.57700 1.71944 5.58467 +H -1.16810 2.29631 4.29351 +O 9.78623 -1.22461 5.88911 +H 9.05533 -0.91721 5.33231 +H 10.59603 -1.00085 5.39957 +O 1.78731 -5.40285 -2.77723 +H 2.33162 -5.12910 -2.00467 +H 0.89681 -5.12748 -2.70535 +O -2.75590 -8.62956 -0.10520 +H -2.53979 -8.69428 -1.07891 +H -2.75324 -7.69016 0.12631 +O 9.87767 -4.00367 7.00969 +H 9.30537 -3.91345 7.71858 +H 9.86640 -3.07612 6.67277 +O 1.36270 2.71836 3.60327 +H 0.90987 3.43987 3.16458 +H 0.69390 2.17126 4.04330 +O 7.35720 -5.27057 -1.72224 +H 8.03476 -6.10104 -1.79227 +H 6.40744 -5.61367 -2.01308 +O 7.59285 -3.91299 1.89032 +H 6.71605 -4.09193 1.42394 +H 7.44293 -4.07392 2.84248 +O -0.53502 -7.32429 -1.57639 +H 0.08940 -6.74166 -2.03905 +H -0.92479 -7.79351 -2.35343 +O 6.33684 6.38743 -5.76835 +H 5.27875 6.21603 -5.54541 +H 6.28403 7.30291 -6.28440 +O 4.69882 -1.31516 6.09464 +H 4.31123 -1.15051 5.12558 +H 4.03848 -1.19721 6.76146 +O 3.70821 -4.04859 4.85959 +H 3.88830 -4.26209 3.90588 +H 3.41156 -4.85543 5.33543 +O 4.25159 -7.25513 3.40025 +H 3.80863 -6.84649 4.18355 +H 4.58665 -8.16468 3.69969 +O 2.85185 -0.22288 -0.08384 +H 2.30198 0.32795 0.57462 +H 3.49964 0.50183 -0.31096 +O 0.71578 0.75467 -1.03772 +H 0.48930 1.73621 -0.79676 +H -0.11147 0.47379 -1.50236 +O 3.86173 -5.86884 0.83708 +H 3.02686 -6.20624 0.38164 +H 3.60762 -6.18672 1.72461 +O -2.65909 1.61105 2.65709 +H -2.81796 1.41394 1.66795 +H -2.90099 2.59787 2.79689 +O 8.58320 -0.93140 3.69116 +H 8.51457 -1.71811 3.08024 +H 9.40919 -0.52395 3.22850 +O 2.00819 -1.77043 1.77406 +H 1.71599 -2.29317 2.51221 +H 2.88786 -2.15737 1.53734 +O -1.21196 4.38114 0.57505 +H -1.88725 5.08448 0.43844 +H -1.31330 3.95262 -0.28572 +O 6.62006 -6.28562 3.52156 +H 6.70557 -5.37221 4.07543 +H 5.67024 -6.53243 3.51712 +O 4.55162 -4.02218 2.45618 +H 4.78639 -3.09848 2.15965 +H 3.76492 -4.29938 1.84435 +O -1.58811 -3.45511 4.54425 +H -2.07874 -3.09246 5.28050 +H -0.94080 -4.03592 4.85498 +O 0.63844 5.84407 -0.58258 +H 0.33058 6.12957 0.29606 +H 1.44170 6.38939 -0.65771 +O 13.89937 3.85311 -4.62853 +H 13.58234 2.94223 -4.24959 +H 14.94280 3.89592 -4.43418 +O 1.45155 -9.85714 -4.86694 +H 2.35131 -9.93790 -5.24325 +H 1.00248 -10.03331 -5.77904 +O 2.10425 -2.89321 -3.62158 +H 1.47224 -2.48362 -2.86866 +H 2.18045 -2.09609 -4.16680 +O 5.30876 -9.33887 2.23872 +H 6.09707 -9.59732 2.71391 +H 5.36099 -10.01325 1.53512 +O 9.39110 -6.28070 3.25110 +H 8.98146 -6.14406 4.06255 +H 8.78207 -5.97081 2.67205 +O 6.25165 -8.48610 -5.29389 +H 6.81062 -9.32378 -5.41835 +H 6.47210 -7.92782 -5.96594 +O -3.15468 -3.34260 7.11828 +H -2.83364 -4.08200 7.65508 +H -3.63428 -3.76480 6.37405 +O 5.85238 -8.41894 -2.66855 +H 5.35988 -8.45234 -1.87962 +H 5.37565 -8.88515 -3.35133 +O -4.47590 -1.40335 3.66515 +H -3.56824 -1.01032 3.81598 +H -4.73962 -1.16543 2.71828 +O -0.20781 -8.30570 1.23188 +H -0.68347 -8.80535 0.48392 +H -0.61830 -7.73467 1.86794 +O 4.95749 4.52203 -1.53048 +H 4.64077 5.16432 -2.29082 +H 4.44398 3.75315 -1.76902 +O -1.18170 -0.41798 -12.61310 +H -0.94931 -0.26291 -13.63669 +H -1.43151 -1.36626 -12.50848 +O 4.37654 -3.87984 -3.11203 +H 3.36699 -3.74856 -3.32174 +H 4.73860 -3.44669 -3.96314 +O 1.47263 -5.10769 2.05248 +H 1.54376 -5.28591 3.06801 +H 0.73852 -4.40355 2.11733 +O 0.57171 0.08269 2.96703 +H 1.33511 -0.28899 2.60400 +H 0.39918 0.95384 2.48030 +O 4.82014 1.75266 -0.26475 +H 4.07740 2.26716 -0.04860 +H 5.55096 2.23000 0.36991 +O 1.26659 -4.90102 -5.18088 +H 0.71571 -5.68172 -5.03880 +H 1.78228 -4.86123 -4.40607 +O -7.57618 -3.41768 -0.23405 +H -7.16860 -4.28058 0.15792 +H -6.80151 -2.90991 -0.56491 +O 6.24921 -6.16862 -4.16104 +H 7.07600 -6.28218 -4.74638 +H 6.36108 -6.98816 -3.57694 +O -1.82911 1.56633 -3.40176 +H -2.45012 2.25119 -3.81374 +H -2.40852 0.75307 -3.27997 +O 1.71669 3.71840 -0.28443 +H 1.27373 4.74944 -0.21805 +H 1.17547 3.28611 0.29122 +O 8.46853 -3.09340 9.86116 +H 7.80954 -2.56880 10.22497 +H 9.34209 -2.47122 9.85476 +O 3.21682 -7.79589 -1.99707 +H 2.52837 -7.35831 -1.41162 +H 2.92784 -8.70634 -2.22468 +O -3.96971 -0.48422 -0.87321 +H -4.71266 -0.93801 -1.27585 +H -3.40046 0.07288 -1.44726 +O 2.58880 0.07464 -2.64410 +H 1.88211 0.38311 -3.18472 +H 1.99881 -0.03955 -1.64188 +O -3.19736 -0.62180 -3.87710 +H -2.95370 -1.51924 -3.42177 +H -4.00833 -0.93762 -4.45389 +O 4.86152 -1.55101 1.42393 +H 5.64113 -1.93118 0.83995 +H 4.42948 -1.03684 0.61612 +O 0.96100 -1.84820 -1.40869 +H 0.12950 -1.31463 -1.51719 +H 1.27479 -1.83709 -0.53915 +O -1.55890 -6.13475 5.77682 +H -0.95828 -6.74283 6.34991 +H -1.41913 -5.28777 6.20053 +O 6.38516 3.66860 0.78566 +H 6.58667 4.01604 1.64321 +H 5.42592 3.87325 0.63911 +O 7.59422 -0.83492 1.07614 +H 7.07118 -1.52087 1.49718 +H 7.19591 -0.75122 0.17345 +O 3.47168 -0.43168 3.60482 +H 3.09120 -1.22210 3.21392 +H 3.70663 0.14389 2.92538 +O -0.36322 -3.35602 1.73591 +H -1.32945 -3.51529 1.69406 +H -0.17779 -2.37533 1.36604 +O 5.81550 6.35896 10.60725 +H 5.04874 5.77496 10.58989 +H 6.38013 6.03712 9.91339 +O 1.14085 -12.62231 4.16390 +H 1.78212 -13.35146 4.36508 +H 0.23752 -13.05745 4.08631 +O -0.35190 -11.38652 0.43131 +H -1.00022 -11.03186 1.01782 +H 0.38267 -10.78230 0.46692 diff --git a/ipi/__init__.py b/ipi/__init__.py index 1b337369a..196aa6995 100644 --- a/ipi/__init__.py +++ b/ipi/__init__.py @@ -12,6 +12,7 @@ "inputs", "interfaces", "utils", + "pes", "ipi_global_settings", "install_driver", "read_output", diff --git a/ipi/engine/forcefields.py b/ipi/engine/forcefields.py index 827d92b6a..d764902b6 100644 --- a/ipi/engine/forcefields.py +++ b/ipi/engine/forcefields.py @@ -23,11 +23,9 @@ from ipi.utils.io import read_file from ipi.utils.units import unit_to_internal from ipi.utils.distance import vector_separation +from ipi.pes import __drivers__ -try: - import plumed -except ImportError: - plumed = None +plumed = None class ForceRequest(dict): @@ -391,6 +389,58 @@ def evaluate(self, request): request["status"] = "Done" +class FFDirect(FFEval): + def __init__( + self, + latency=1.0, + offset=0.0, + name="", + pars=None, + dopbc=False, + active=np.array([-1]), + threaded=False, + pes="dummy", + ): + """Initialises FFDirect. + + Args: + latency: The number of seconds the socket will wait before updating + the client list. + offset: A constant offset subtracted from the energy value given by the + client. + name: The name of the forcefield. + pars: A dictionary used to initialize the forcefield, if required. + Of the form {'name1': value1, 'name2': value2, ... }. + dopbc: Decides whether or not to apply the periodic boundary conditions + before sending the positions to the client code. + active: Indexes of active atoms in this forcefield + + """ + + super().__init__(latency, offset, name, pars, dopbc, active, threaded) + + self.pes = pes + try: + self.driver = __drivers__[self.pes](verbose=verbosity.high, **pars) + except ImportError: + # specific errors have already been triggered + raise + except Exception as err: + print(f"Error setting up PES mode {self.pes}") + print(__drivers__[self.pes].__doc__) + print("Error trace: ") + raise err + + def evaluate(self, request): + results = list(self.driver(request["cell"][0], request["pos"].reshape(-1, 3))) + + # ensure forces and virial have the correct shape to fit the results + results[1] = results[1].reshape(-1) + results[2] = results[2].reshape(3, 3) + request["result"] = results + request["status"] = "Done" + + class FFLennardJones(FFEval): """Basic fully pythonic force provider. @@ -409,12 +459,14 @@ class FFLennardJones(FFEval): def __init__( self, - latency=1.0e-3, + latency=1.0, offset=0.0, name="", pars=None, - dopbc=False, - threaded=False, + dopbc=True, + active=np.array([-1]), + threaded=True, + interface=None, ): """Initialises FFLennardJones. @@ -430,7 +482,7 @@ def __init__( # a socket to the communication library is created or linked super(FFLennardJones, self).__init__( - latency, offset, name, pars, dopbc=dopbc, threaded=threaded + latency, offset, name, pars, dopbc=dopbc, threaded=threaded, active=active ) self.epsfour = float(self.pars["eps"]) * 4 self.sixepsfour = 6 * self.epsfour @@ -678,8 +730,11 @@ def __init__( pars: Optional dictionary, giving the parameters needed by the driver. """ + global plumed # a socket to the communication library is created or linked - if plumed is None: + try: + import plumed + except ImportError: raise ImportError( "Cannot find plumed libraries to link to a FFPlumed object/" ) @@ -863,6 +918,14 @@ def __init__( """ + warning( + """ + is deprecated and might be removed in a future release of i-PI. + If you are interested in using it, please help port it to the PES + infrastructure. + """ + ) + from yaff import System, ForceField, log import codecs import locale @@ -955,6 +1018,14 @@ def __init__( """ + warning( + """ + is deprecated and might be removed in a future release of i-PI. + If you are interested in using it, please help port it to the PES + infrastructure. + """ + ) + # a socket to the communication library is created or linked super(FFsGDML, self).__init__( latency, offset, name, pars, dopbc, threaded=threaded diff --git a/ipi/inputs/forcefields.py b/ipi/inputs/forcefields.py index a8fcd6467..f3b8e0757 100644 --- a/ipi/inputs/forcefields.py +++ b/ipi/inputs/forcefields.py @@ -11,6 +11,7 @@ from ipi.engine.forcefields import ( ForceField, FFSocket, + FFDirect, FFLennardJones, FFDebye, FFPlumed, @@ -21,6 +22,7 @@ FFCavPhSocket, ) from ipi.interfaces.sockets import InterfaceSocket +from ipi.pes import __drivers__ import ipi.engine.initializer from ipi.inputs.initializer import * from ipi.utils.inputvalue import * @@ -28,6 +30,7 @@ __all__ = [ "InputFFSocket", + "InputFFDirect", "InputFFLennardJones", "InputFFDebye", "InputFFPlumed", @@ -135,6 +138,8 @@ def store(self, ff): self.activelist.store(ff.active) self.threaded.store(ff.threaded) + _FFCLASS = ForceField + def fetch(self): """Creates a ForceField object. @@ -144,7 +149,7 @@ def fetch(self): super(InputForceField, self).fetch() - return ForceField( + return self._FFCLASS( pars=self.parameters.fetch(), name=self.name.fetch(), latency=self.latency.fetch(), @@ -336,37 +341,58 @@ def check(self): raise ValueError("Negative timeout parameter specified.") -class InputFFLennardJones(InputForceField): +class InputFFDirect(InputForceField): + fields = { + "pes": ( + InputValue, + { + "dtype": str, + "default": "dummy", + "options": list(__drivers__.keys()), + "help": "Type of PES that should be used to evaluate the forcefield", + }, + ), + } + fields.update(InputForceField.fields) + attribs = {} attribs.update(InputForceField.attribs) - default_help = """Simple, internal LJ evaluator without cutoff, neighbour lists or minimal image convention. - Expects standard LJ parameters, e.g. { eps: 0.1, sigma: 1.0 }. """ - default_label = "FFLJ" + default_help = """ Direct potential that evaluates forces through a Python + call, using PES providers from a list of possible external codes. The available + PES interfaces are listed into the `ipi/pes` folder, and are the same available + for the Python driver. The `` field should contain a dictionary + of the specific option of the chosen PES. + """ + default_label = "FFDirect" def store(self, ff): - super(InputFFLennardJones, self).store(ff) + super().store(ff) + self.pes.store(ff.pes) def fetch(self): - super(InputFFLennardJones, self).fetch() + super().fetch() - return FFLennardJones( + return FFDirect( pars=self.parameters.fetch(), name=self.name.fetch(), latency=self.latency.fetch(), offset=self.offset.fetch(), dopbc=self.pbc.fetch(), threaded=self.threaded.fetch(), + pes=self.pes.fetch(), ) - if self.slots.fetch() < 1 or self.slots.fetch() > 5: - raise ValueError( - "Slot number " + str(self.slots.fetch()) + " out of acceptable range." - ) - if self.latency.fetch() < 0: - raise ValueError("Negative latency parameter specified.") - if self.timeout.fetch() < 0.0: - raise ValueError("Negative timeout parameter specified.") + +class InputFFLennardJones(InputForceField): + attribs = {} + attribs.update(InputForceField.attribs) + + default_help = """Simple, internal LJ evaluator without cutoff, neighbour lists or minimal image convention. + Expects standard LJ parameters, e.g. { eps: 0.1, sigma: 1.0 }. """ + default_label = "FFLJ" + + _FFCLASS = FFLennardJones class InputFFdmd(InputForceField): @@ -445,7 +471,7 @@ class InputFFDebye(InputForceField): "default": input_default(factory=np.zeros, args=(0,)), "help": "Specifies the Hessian of the harmonic potential. " "Default units are atomic. Units can be specified only by xml attribute. " - "Implemented options are: 'atomic_unit', 'ev/ang\^2'", + r"Implemented options are: 'atomic_unit', 'ev/ang^2'", "dimension": "hessian", }, ), @@ -747,6 +773,7 @@ class InputFFCommittee(InputForceField): dynamic = { "ffsocket": (InputFFSocket, {"help": InputFFSocket.default_help}), + "ffdirect": (InputFFDirect, {"help": InputFFDirect.default_help}), "fflj": (InputFFLennardJones, {"help": InputFFLennardJones.default_help}), "ffdebye": (InputFFDebye, {"help": InputFFDebye.default_help}), "ffplumed": (InputFFPlumed, {"help": InputFFPlumed.default_help}), diff --git a/ipi/inputs/simulation.py b/ipi/inputs/simulation.py index 56b8666a3..796316d59 100644 --- a/ipi/inputs/simulation.py +++ b/ipi/inputs/simulation.py @@ -159,6 +159,10 @@ class InputSimulation(Input): iforcefields.InputFFSocket, {"help": iforcefields.InputFFSocket.default_help}, ), + "ffdirect": ( + iforcefields.InputFFDirect, + {"help": iforcefields.InputFFDirect.default_help}, + ), "fflj": ( iforcefields.InputFFLennardJones, {"help": iforcefields.InputFFLennardJones.default_help}, @@ -246,6 +250,10 @@ def store(self, simul): _iobj = iforcefields.InputFFSocket() _iobj.store(_obj) self.extra[_ii] = ("ffsocket", _iobj) + elif isinstance(_obj, eforcefields.FFDirect): + _iobj = iforcefields.InputFFDirect() + _iobj.store(_obj) + self.extra[_ii] = ("ffdirect", _iobj) elif isinstance(_obj, eforcefields.FFLennardJones): _iobj = iforcefields.InputFFLennardJones() _iobj.store(_obj) @@ -322,17 +330,18 @@ def fetch(self): # of system objects with the desired properties set # automatically to many values. syslist += v.fetch() - elif ( - k == "ffsocket" - or k == "fflj" - or k == "ffdebye" - or k == "ffdmd" - or k == "ffplumed" - or k == "ffsgdml" - or k == "ffyaff" - or k == "ffcommittee" - or k == "ffcavphsocket" - ): + elif k in [ + "ffsocket", + "ffdirect", + "fflj", + "ffdebye", + "ffdmd", + "ffplumed", + "ffsgdml", + "ffyaff", + "ffcommittee", + "ffcavphsocket", + ]: new_ff = v.fetch() if k == "ffsocket": # overrides ffsocket prefix diff --git a/drivers/py/pes/__init__.py b/ipi/pes/__init__.py similarity index 100% rename from drivers/py/pes/__init__.py rename to ipi/pes/__init__.py diff --git a/drivers/py/pes/ase.py b/ipi/pes/ase.py similarity index 70% rename from drivers/py/pes/ase.py rename to ipi/pes/ase.py index 7d5597a52..567c4e4e7 100644 --- a/drivers/py/pes/ase.py +++ b/ipi/pes/ase.py @@ -1,48 +1,45 @@ """Interface with ASE calculators""" -import sys import numpy as np from .dummy import Dummy_driver from ipi.utils.units import unit_to_internal, unit_to_user from ipi.utils.messages import warning -try: - from ase.io import read -except ImportError: - warning("Could not find or import the ASE module") - MetatensorCalculator = None + +read = None __DRIVER_NAME__ = "ase" __DRIVER_CLASS__ = "ASEDriver" -ERROR_MSG = """ -This ASE driver requires specification of and ASE calculator -and an ASE-readable template file that describes the chemical makeup of the structure. - -Example: python driver.py -m ase -u -o template.xyz,model_parameters -""" - class ASEDriver(Dummy_driver): - """Abstract base class using an arbitrary ASE calculator as i-pi driver""" - - def __init__(self, args=None, verbose=False, error_msg=ERROR_MSG): - super().__init__(args, verbose, error_msg=error_msg) - - def check_arguments(self): + """ + Base class using an arbitrary ASE calculator as i-pi driver. + Should not be called directly as it does not set a calculator. + + Parameters: + :param verbose: bool, whether to print verbose output + :param template: string, ASE-readable filename where to get the structure data from + """ + + def __init__(self, template, *args, **kwargs): + global read + try: + from ase.io import read + except ImportError: + warning("Could not find or import the ASE module") + + self.template = template + super().__init__(*args, **kwargs) + + def check_parameters(self): """Check the arguments required to run the driver This loads the potential and atoms template in metatensor """ - if len(self.args) >= 1: - self.template = self.args[0] - else: - sys.exit(self.error_msg) - self.template_ase = read(self.template) - self.ase_calculator = None def __call__(self, cell, pos): @@ -63,7 +60,9 @@ def __call__(self, cell, pos): structure.calc = self.ase_calculator # Do the actual calculation - properties = structure.get_properties(["energy", "forces", "stress"]) + self.ase_calculator.calculate(atoms=structure) + properties = self.ase_calculator.results + pot = properties["energy"] force = properties["forces"] stress = properties["stress"] diff --git a/drivers/py/pes/bath.py b/ipi/pes/bath.py similarity index 79% rename from drivers/py/pes/bath.py rename to ipi/pes/bath.py index f4d62d95e..c49c63de6 100644 --- a/drivers/py/pes/bath.py +++ b/ipi/pes/bath.py @@ -2,22 +2,29 @@ import numpy as np -__DRIVER_NAME__ = None -__DRIVER_CLASS__ = "driver_tools" +from ipi.utils.messages import verbosity, warning + +__DRIVER_NAME__ = "bath" +__DRIVER_CLASS__ = "Harmonic_Bath_explicit" class Harmonic_Bath_explicit(object): """Explicit description of an Harmonic bath""" - def __init__(self, nbath, parameters): + def __init__(self, nbath, m, eta0, eps1, eps2, deltaQ, w_c, *args, **kwargs): + warning( + "THIS PES HAS NOT BEEN TESTED FOLLOWING CONVERSION TO THE NEW PES API.", + verbosity.low, + ) + super().__init__(*args, **kwargs) + self.nbath = nbath - self.m = parameters["m"] - # self.delta = parameters["delta"] - self.eta0 = parameters["eta0"] - self.eps1 = parameters["eps1"] - self.eps2 = parameters["eps2"] - self.deltaQ = parameters["deltaQ"] - self.w_c = parameters["w_c"] + self.m = m + self.eta0 = eta0 + self.eps1 = eps1 + self.eps2 = eps2 + self.deltaQ = deltaQ + self.w_c = w_c self.set_ci_and_wi() diff --git a/drivers/py/pes/doubledoublewell.py b/ipi/pes/doubledoublewell.py similarity index 71% rename from drivers/py/pes/doubledoublewell.py rename to ipi/pes/doubledoublewell.py index 94b5c90e5..e4f633639 100644 --- a/drivers/py/pes/doubledoublewell.py +++ b/ipi/pes/doubledoublewell.py @@ -28,7 +28,7 @@ class DDW_with_explicit_bath_driver(Dummy_driver): - """Adds to a double-double well (DDW) potential coupled to two (explicit) harmonic baths. + r"""Adds to a double-double well (DDW) potential coupled to two (explicit) harmonic baths. pos[0:2] = DDW pos[2:n//2+1] = bath1 pos[n//2+1:] = bath2 @@ -47,49 +47,61 @@ class DDW_with_explicit_bath_driver(Dummy_driver): ! and ! ! DDW(q1,q2) = DW(q1) + DW(q2) + C(q1q2)^2 - """ - def __init__(self, args=None, verbose=None): - self.error_msg = """\nDW+explicit_bath driver expects 11 arguments.\n - Example: python driver.py -m DoubleWell_with_explicit_bath -o wb1 (cm^-1) V1 (cm^-1) wb2 (cm^-1) V2 (cm^-1) coupling(au) mass delta(\AA) eta0 eps1 eps2 deltaQ omega_c(cm^-1) \n - python driver.py -m DoubleWell -o 500,2085,500,2085,0.1,1837,0.00,1,0,0,1,500\n""" - super(DDW_with_explicit_bath_driver, self).__init__( - args, error_msg=self.error_msg - ) - self.init = False + DW+explicit_bath driver expects 11 arguments.\n + Example: + i-pi-py_driver.py -m DoubleWell_with_explicit_bath -o wb1 (cm^-1) V1 (cm^-1) wb2 (cm^-1) V2 (cm^-1) coupling(au) mass delta(\AA) eta0 eps1 eps2 deltaQ omega_c(cm^-1) \n + i-pi-py_driver.py -m DoubleWell -o 500,2085,500,2085,0.1,1837,0.00,1,0,0,1,500 + """ - def check_arguments(self): - """Function that checks the arguments required to run the driver""" + def __init__( + self, + wb1=None, + v1=None, + wb2=None, + v2=None, + C=None, + m=None, + delta=None, + eta0=None, + eps1=None, + eps2=None, + deltaQ=None, + w_c=None, + *args, + **kwargs + ): + self.init = False try: - param = list(map(float, self.args)) - assert len(param) == 12 - wb1 = param[0] * invcm2au - v1 = param[1] * invcm2au - wb2 = param[2] * invcm2au - v2 = param[3] * invcm2au - self.C = param[4] - self.m = param[5] - self.delta = param[6] * A2au + wb1 = wb1 * invcm2au + v1 = v1 * invcm2au + wb2 = wb2 * invcm2au + v2 = v2 * invcm2au + self.C = C + self.m = m + self.delta = delta * A2au self.bath_parameters = {} self.bath_parameters["m"] = self.m + self.bath_parameters["eta0"] = eta0 + self.bath_parameters["eps1"] = eps1 + self.bath_parameters["eps2"] = eps2 + self.bath_parameters["deltaQ"] = deltaQ + self.bath_parameters["w_c"] = w_c * invcm2au self.bath_parameters["delta"] = self.delta - self.bath_parameters["eta0"] = param[7] - self.bath_parameters["eps1"] = param[8] - self.bath_parameters["eps2"] = param[9] - self.bath_parameters["deltaQ"] = param[10] - self.bath_parameters["w_c"] = param[11] * invcm2au + # def __init__(self, nbath, m, eta0, eps1, eps2, deltaQ, w_c, *args, **kwargs): except: print("Received arguments:") - sys.exit(self.error_msg) + sys.exit(self.__doc__) self.A1 = -0.5 * self.m * (wb1) ** 2 self.B1 = ((self.m**2) * (wb1) ** 4) / (16 * v1) self.A2 = -0.5 * self.m * (wb2) ** 2 self.B2 = ((self.m**2) * (wb2) ** 4) / (16 * v2) + super().__init__(*args, **kwargs) def __call__(self, cell, pos): """DoubleWell potential""" diff --git a/drivers/py/pes/doublewell.py b/ipi/pes/doublewell.py similarity index 73% rename from drivers/py/pes/doublewell.py rename to ipi/pes/doublewell.py index b75dad204..10987414f 100644 --- a/drivers/py/pes/doublewell.py +++ b/ipi/pes/doublewell.py @@ -28,15 +28,14 @@ class DoubleWell_driver(Dummy_driver): - def __init__(self, args=None, verbose=None): - self.error_msg = """\nDW driver accepts 0 or 4 arguments.\nExample: python driver.py -m DoubleWell -o omega_b (cm^-1) V0 (cm^-1) mass(a.u) delta(angs) \n + """ + DW driver accepts 0 or 4 arguments.\nExample: python driver.py -m DoubleWell -o omega_b (cm^-1) V0 (cm^-1) mass(a.u) delta(angs) \n python driver.py -m DoubleWell -o 500,2085,1837,0.00 \n""" - super(DoubleWell_driver, self).__init__(args, error_msg=self.error_msg) - def check_arguments(self): - """Function that checks the arguments required to run the driver""" - self.k = 1837.36223469 * (3800.0 / 219323.0) ** 2 - if self.args == "": + def __init__(self, w_b=None, v0=None, m=None, delta=None, *args, **kwargs): + + if w_b == None or v0 == None or m == None or delta == None: + print("using default values from Craig-JCP-2005") # We used Craig's values (J. Chem. Phys. 122, 084106, 2005) w_b = 500 * invcm2au # Tc = 115K v0 = 2085 * invcm2au @@ -44,17 +43,16 @@ def check_arguments(self): self.delta = 00 else: try: - param = list(map(float, self.args)) - assert len(param) == 4 - w_b = param[0] * invcm2au - v0 = param[1] * invcm2au - m = param[2] - self.delta = param[3] * A2au + w_b = w_b * invcm2au + v0 = v0 * invcm2au + self.delta = delta * A2au except: - sys.exit(self.error_msg) + sys.exit(self.__doc__) + self.k = 1837.36223469 * (3800.0 / 219323.0) ** 2 self.A = -0.5 * m * (w_b) ** 2 self.B = ((m**2) * (w_b) ** 4) / (16 * v0) + super().__init__(*args, **kwargs) def __call__(self, cell, pos): """DoubleWell potential l""" diff --git a/drivers/py/pes/doublewell_with_bath.py b/ipi/pes/doublewell_with_bath.py similarity index 65% rename from drivers/py/pes/doublewell_with_bath.py rename to ipi/pes/doublewell_with_bath.py index d5b8567f2..a79354f8e 100644 --- a/drivers/py/pes/doublewell_with_bath.py +++ b/ipi/pes/doublewell_with_bath.py @@ -30,50 +30,57 @@ class DoubleWell_with_explicit_bath_driver(Dummy_driver): - """Adds to the double well potential an explicit harmonic bath. First dof correpond to the DW, the rest to the bath discretization + r"""Adds to the double well potential an explicit harmonic bath. First dof correpond to the DW, the rest to the bath discretization ! V(q,x1,..,xn) = DW(q) + ! sum_2^(3*N) [ 0.5 m w_i^2(q - (c_i s(q))/(m w_i)^2)^2 ] ! s(q) = q *sd(q) ! sd(q) = [1+eps1*exp( q^2 / (2 deltaQ^2) ) ] + eps2 tanh(q/deltaQ) ! If eps1=eps2=0 then sd(q) =1 and s(q) = q --->Spatially independent bath - """ - def __init__(self, args=None, verbose=None): - self.error_msg = """\nDW+explicit_bath driver expects 9 arguments.\n + DW+explicit_bath driver expects 9 arguments. Example: python driver.py -m DoubleWell_with_explicit_bath -o omega_b (cm^-1) V0 (cm^-1) mass delta(\AA) eta0 eps1 eps2 deltaQ omega_c(cm^-1) \n - python driver.py -m DoubleWell -o 500,2085,1837,0.00,1,0,0,1,500\n""" - super(DoubleWell_with_explicit_bath_driver, self).__init__( - args, error_msg=self.error_msg - ) + python driver.py -m DoubleWell -o 500,2085,1837,0.00,1,0,0,1,500 + """ - self.init = False + def __init__( + self, + w_b=None, + v0=None, + m=None, + delta=None, + eta0=None, + eps1=None, + eps2=None, + deltaQ=None, + w_c=None, + *args, + **kwargs + ): - def check_arguments(self): - """Function that checks the arguments required to run the driver""" + self.init = False try: - param = list(map(float, self.args)) - assert len(param) == 9 - w_b = param[0] * invcm2au - v0 = param[1] * invcm2au - self.m = param[2] - self.delta = param[3] * A2au + w_b = w_b * invcm2au + v0 = v0 * invcm2au + self.m = m + self.delta = delta * A2au self.bath_parameters = {} - self.bath_parameters["m"] = param[2] + self.bath_parameters["m"] = self.m - self.bath_parameters["eta0"] = param[4] - self.bath_parameters["eps1"] = param[5] - self.bath_parameters["eps2"] = param[6] - self.bath_parameters["deltaQ"] = param[7] - self.bath_parameters["w_c"] = param[8] * invcm2au + self.bath_parameters["eta0"] = eta0 + self.bath_parameters["eps1"] = eps1 + self.bath_parameters["eps2"] = eps2 + self.bath_parameters["deltaQ"] = deltaQ + self.bath_parameters["w_c"] = w_c * invcm2au except: - sys.exit(self.error_msg) + sys.exit(self.__doc__) self.A = -0.5 * self.m * (w_b) ** 2 self.B = ((self.m**2) * (w_b) ** 4) / (16 * v0) + super().__init__(*args, **kwargs) def __call__(self, cell, pos): """DoubleWell potential""" @@ -85,7 +92,7 @@ def __call__(self, cell, pos): if not self.init: self.nbath = np.size(x) - self.bath = Harmonic_Bath_explicit(self.nbath, self.bath_parameters) + self.bath = Harmonic_Bath_explicit(self.nbath, **self.bath_parameters) # Harmonic bath pot, fq, fx = self.bath(q, x) diff --git a/drivers/py/pes/doublewell_with_friction.py b/ipi/pes/doublewell_with_friction.py similarity index 71% rename from drivers/py/pes/doublewell_with_friction.py rename to ipi/pes/doublewell_with_friction.py index dfacdb7b8..d456cfb43 100644 --- a/drivers/py/pes/doublewell_with_friction.py +++ b/ipi/pes/doublewell_with_friction.py @@ -1,7 +1,5 @@ """ Harmonic potential """ -import sys - try: from .doublewell import DoubleWell_driver except: @@ -10,6 +8,7 @@ import numpy as np from ipi.utils import units import json +import sys __DRIVER_NAME__ = "DW_friction" @@ -29,42 +28,48 @@ class DoubleWell_with_friction_driver(DoubleWell_driver): - """Adds to the double well potential the calculation of the friction tensor. + r"""Adds to the double well potential the calculation of the friction tensor. friction(q) = eta0 [\partial sd(q) \partial q ]^2 with q = position, and sd(q) = [1+eps1 exp( (q-0)^2 / (2deltaQ^2) ) ] + eps2 tanh(q/deltaQ) - """ - def __init__(self, args=None, verbose=None): - self.error_msg = """\nDW+fric driver expects 8 arguments.\n - Example: python driver.py -m DoubleWell_with_fric -o omega_b (cm^-1) V0 (cm^-1) mass delta(\AA) eta0 eps1 eps2 deltaQ \n - python driver.py -m DoubleWell -o 500,2085,1837,0.00,1,0,0,1\n""" - self.args = args.split(",") - self.verbose = verbose - self.check_arguments() + DW+fric driver expects 8 arguments. + Example: python driver.py -m DoubleWell_with_fric -o omega_b (cm^-1) V0 (cm^-1) mass delta(\AA) eta0 eps1 eps2 deltaQ + python driver.py -m DoubleWell -o 500,2085,1837,0.00,1,0,0,1 + """ - def check_arguments(self): - """Function that checks the arguments required to run the driver""" + def __init__( + self, + w_b=None, + v0=None, + m=None, + eta0=None, + eps1=None, + eps2=None, + delta=None, + deltaQ=None, + *args, + **kwargs + ): - self.k = 1837.36223469 * (3800.0 / 219323.0) ** 2 try: - param = list(map(float, self.args)) - assert len(param) == 8 - w_b = param[0] * invcm2au - v0 = param[1] * invcm2au - m = param[2] - self.delta = param[3] * A2au - self.eta0 = param[4] - self.eps1 = param[5] - self.eps2 = param[6] - self.deltaQ = param[7] + w_b = w_b * invcm2au + v0 = v0 * invcm2au + self.delta = delta * A2au + self.eta0 = eta0 + self.eps1 = eps1 + self.eps2 = eps2 + self.deltaQ = deltaQ + self.k = 1837.36223469 * (3800.0 / 219323.0) ** 2 + self.A = -0.5 * m * (w_b) ** 2 + self.B = ((m**2) * (w_b) ** 4) / (16 * v0) + except: - sys.exit(self.error_msg) + sys.exit(self.__doc__) - self.A = -0.5 * m * (w_b) ** 2 - self.B = ((m**2) * (w_b) ** 4) / (16 * v0) + super().__init__(*args, **kwargs) def check_dimensions(self, pos): """Functions that checks dimensions of the received position""" diff --git a/drivers/py/pes/driverdipole.py b/ipi/pes/driverdipole.py similarity index 95% rename from drivers/py/pes/driverdipole.py rename to ipi/pes/driverdipole.py index be0929042..2a87b9242 100644 --- a/drivers/py/pes/driverdipole.py +++ b/ipi/pes/driverdipole.py @@ -4,6 +4,9 @@ import json import numpy as np import warnings + +from ipi.utils.messages import verbosity, warning + import importlib from .dummy import Dummy_driver @@ -118,6 +121,9 @@ def get_model(instructions, parameters: str): class driverdipole_driver(Dummy_driver): + """The parameters of 'driverdipole_driver' are not correctly formatted. \ + They should be two or three strings, separated by a comma.""" + opts_default = { "dipole": { "send": True, # whether to send the dipole to i-PI @@ -131,19 +137,21 @@ class driverdipole_driver(Dummy_driver): "restart": False, # whether remove the files (if already existing) where the dipole and BEC will be saved. } - def __init__(self, args=None): - self.error_msg = """The parameters of 'driverdipole_driver' are not correctly formatted. \ - They should be two or three strings, separated by a comma.""" + def __init__(self, *args, **kwargs): + warning( + "THIS PES HAS NOT BEEN TESTED FOLLOWING CONVERSION TO THE NEW PES API.", + verbosity.low, + ) self.opts = dict() self.count = 0 - super().__init__(args) + super().__init__(*args, **kwargs) - def check_arguments(self): + def check_parameters(self): """Check the arguments required to run the driver.""" try: - arglist = self.args.split(",") + arglist = self.args except ValueError: - sys.exit(self.error_msg) + sys.exit(self.__doc__) if len(arglist) >= 2: info_file = arglist[0] # json file to properly allocate a 'model' object @@ -154,7 +162,7 @@ def check_arguments(self): print("\tNo options file provided: using the default values") opts_file = None else: - sys.exit(self.error_msg) # to be modified + sys.exit(self._error_msg) # to be modified print("\n\tThe driver is 'driverdipole_driver'") print("\tLoading model ...") diff --git a/drivers/py/pes/dummy.py b/ipi/pes/dummy.py similarity index 71% rename from drivers/py/pes/dummy.py rename to ipi/pes/dummy.py index 457c624a3..83430a93c 100644 --- a/drivers/py/pes/dummy.py +++ b/ipi/pes/dummy.py @@ -6,18 +6,23 @@ class Dummy_driver(object): - """Base class providing the structure of a PES for the python driver.""" + """Base class providing the structure of a PES for the python driver. - def __init__( - self, args="", verbose=False, error_msg="Invalid arguments for the PES" - ): + Command line: + i-pi-py_driver -m dummy [...] + Init arguments: + :param verbose: bool to determine whether the PES should output verbose info. + """ + + def __init__(self, verbose=False, *args, **kwargs): """Initialized dummy drivers""" - self.error_msg = error_msg - self.args = args.split(",") self.verbose = verbose - self.check_arguments() + self.args = args + self.kwargs = kwargs + + self.check_parameters() - def check_arguments(self): + def check_parameters(self): """Dummy function that checks the arguments required to run the driver""" pass diff --git a/drivers/py/pes/elphmod.py b/ipi/pes/elphmod.py similarity index 55% rename from drivers/py/pes/elphmod.py rename to ipi/pes/elphmod.py index efa863131..f4068d1c4 100644 --- a/drivers/py/pes/elphmod.py +++ b/ipi/pes/elphmod.py @@ -3,26 +3,29 @@ import sys from .dummy import Dummy_driver +from ipi.utils.messages import verbosity, warning + __DRIVER_NAME__ = "elphmod" __DRIVER_CLASS__ = "ModelIIIDriver" -ERROR_MSG = """ -A pickled driver instance is required (see elphmod.md.Driver.save). - -Example: python3 driver.py -u -m elphmod -o driver.pickle -""" - class ModelIIIDriver(Dummy_driver): - """Wrapper around elphmod MD driver.""" + """Wrapper around elphmod MD driver. + A pickled driver instance is required (see elphmod.md.Driver.save). - def check_arguments(self): - """Check arguments and load driver instance.""" + Example: python3 driver.py -u -m elphmod -o driver.pickle + """ + def check_parameters(self): + """Check arguments and load driver instance.""" + warning( + "THIS PES HAS NOT BEEN TESTED FOLLOWING CONVERSION TO THE NEW PES API.", + verbosity.low, + ) import elphmod if len(self.args) != 1: - sys.exit(ERROR_MSG) + sys.exit(self.__doc__) self.driver = elphmod.md.Driver.load(self.args[0]) diff --git a/drivers/py/pes/harmonic.py b/ipi/pes/harmonic.py similarity index 60% rename from drivers/py/pes/harmonic.py rename to ipi/pes/harmonic.py index d92f7bac9..df3974815 100644 --- a/drivers/py/pes/harmonic.py +++ b/ipi/pes/harmonic.py @@ -1,33 +1,37 @@ """ Harmonic potential """ -import sys from .dummy import Dummy_driver import numpy as np __DRIVER_NAME__ = "harmonic" __DRIVER_CLASS__ = "Harmonic_driver" -ERROR_MSG = """ -Harmonic driver requires specification of force constant. -Example: python driver.py -m harmonic -u -o 1.3 -""" - class Harmonic_driver(Dummy_driver): - def __init__(self, args=None, verbose=False): - super(Harmonic_driver, self).__init__(args, verbose, error_msg=ERROR_MSG) + """ + Harmonic driver, generating either an isotropic or 3D confining + potential for each atom. + + Command-line: + i-pi-py_driver -m harmonic -u -o 1.3 [...] + i-pi-py_driver -m harmonic -u -o 1.3,2.1,2.3 [...] + + Init parameters: + :param k1: float, spring constant of the oscillator (in a.u.) + :param k2: float, spring constant of the oscillator along y (in a.u.), optional + :param k3: float, spring constant of the oscillator along z (in a.u.), optional + """ - def check_arguments(self): - """Function that checks the arguments required to run the driver""" + def __init__(self, k1, k2=None, k3=None, *args, **kwargs): - if len(self.args) == 1: - self.k = float(self.args[0]) + if k2 == None or k3 == None: + self.k = k1 self.type = "isotropic" - elif len(self.args) == 3: - self.k = np.asarray(list(map(float, self.args))) - self.type = "non-isotropic" else: - sys.exit(self.error_msg) + self.k = np.asarray([k1, k2, k3]) + self.type = "non-isotropic" + + super().__init__(*args, **kwargs) def __call__(self, cell, pos): """Silly harmonic potential""" diff --git a/ipi/pes/mace.py b/ipi/pes/mace.py new file mode 100644 index 000000000..0aea548bb --- /dev/null +++ b/ipi/pes/mace.py @@ -0,0 +1,53 @@ +""" An interface for the [MACE](https://github.com/ACEsuit/mace) calculator """ + +from .ase import ASEDriver + +from ipi.utils.messages import verbosity, warning + +MACECalculator = None + +__DRIVER_NAME__ = "mace" +__DRIVER_CLASS__ = "MACE_driver" + + +class MACE_driver(ASEDriver): + """ + Driver for the MACE MLIPs. + The driver requires specification of a .json model, + and a template file that describes the chemical makeup + of the structure. + + Command-line: + i-pi-py_driver.py -m mace -u -o template=template.xyz,model=model.json + + Parameters: + :param template: string, filename of an ASE-readable structure file + to initialize atomic number and types + :param model: string, filename of the json-formatted model file + """ + + def __init__(self, template, model, device="cpu", *args, **kwargs): + warning( + "THIS PES HAS NOT BEEN TESTED FOLLOWING CONVERSION TO THE NEW PES API.", + verbosity.low, + ) + global MACECalculator + + try: + from mace.calculators import MACECalculator + except: + raise ImportError("Couldn't load mace bindings") + + self.model = model + self.device = device + super().__init__(template, *args, **kwargs) + + def check_parameters(self): + """Check the arguments requuired to run the driver + + This loads the potential and atoms template in MACE + """ + + super().check_parameters() + + self.ase_calculator = MACECalculator(model_paths=self.model, device=self.device) diff --git a/ipi/pes/metatensor.py b/ipi/pes/metatensor.py new file mode 100644 index 000000000..d857c68ad --- /dev/null +++ b/ipi/pes/metatensor.py @@ -0,0 +1,98 @@ +""" +Interface with metatensor +(https://lab-cosmo.github.io/metatensor/latest/atomistic/index.html), that can +be used to perform calculations based on different types of machine learning +potentials +""" + +from ipi.utils.messages import warning + +from .ase import ASEDriver + +MetatensorCalculator = None +mtt = None + +__DRIVER_NAME__ = "metatensor" +__DRIVER_CLASS__ = "MetatensorDriver" + + +class MetatensorDriver(ASEDriver): + """ + Driver for `metatensor` MLIPs + The driver requires specification of a torchscript model, + and a template file that describes the chemical makeup + of the structure. Requires the metatensor-torch library + + Command-line: + i-pi-py_driver -m metatensor -o template=template.xyz,model=model.json [...] + + Parameters: + :param template: string, filename of an ASE-readable structure file + to initialize atomic number and types + :param model: string, filename of the torchscript model file + :param device: string, optional, ["cpu" | "cuda"] + """ + + def __init__( + self, + template, + model, + device="cpu", + extensions="", + check_consistency=False, + *args, + **kwargs, + ): + global MetatensorCalculator, mtt + if MetatensorCalculator is None: + try: + import metatensor.torch as mtt + from metatensor.torch.atomistic.ase_calculator import ( + MetatensorCalculator, + ) + except ImportError as e: + warning(f"Could not find or import metatensor.torch: {e}") + + self.model = model + self.device = device + self.extensions = extensions + self.check_consistency = check_consistency + super().__init__(template, *args, **kwargs) + + def check_parameters(self): + """Check the arguments required to run the driver + + This loads the potential and atoms template in metatensor + """ + + if MetatensorCalculator is None: + raise ImportError("could not import metatensor.torch, is it installed?") + + metatensor_major, metatensor_minor, *_ = mtt.__version__.split(".") + metatensor_major = int(metatensor_major) + metatensor_minor = int(metatensor_minor) + + if metatensor_major != 0 or metatensor_minor < 5: + raise ImportError( + "this code is only compatible with metatensor-torch >= v0.5, " + f"found version v{mtt.__version__} " + f"at '{mtt.__file__}'" + ) + + super().check_parameters() + + self.model_path = self.model + + device = self.device + extensions_directory = self.extensions + check_consistency = self.check_consistency + + self.ase_calculator = MetatensorCalculator( + self.model_path, + device=device, + extensions_directory=extensions_directory, + check_consistency=check_consistency, + ) + + # Show the model metadata to the users + print(self.ase_calculator.metadata()) diff --git a/drivers/py/pes/pet.py b/ipi/pes/pet.py similarity index 53% rename from drivers/py/pes/pet.py rename to ipi/pes/pet.py index f072336e2..7e54c37e3 100644 --- a/drivers/py/pes/pet.py +++ b/ipi/pes/pet.py @@ -1,78 +1,65 @@ """Interface with [PET](https://github.com/serfg/pet) models to run machine learning potentials""" -import sys import numpy as np from .dummy import Dummy_driver from ipi.utils.units import unit_to_internal, unit_to_user from ipi.utils.messages import warning -try: - from pet import SingleStructCalculator as PETCalc - - try: - from ase.io import read - except ImportError: - warning("The PET driver has an ASE dependency") - raise -except ImportError: - warning("Could not find or import the PET module") - PETCalc = None +PETCalc = None +read = None __DRIVER_NAME__ = "pet" __DRIVER_CLASS__ = "PET_driver" class PET_driver(Dummy_driver): - def __init__(self, args=None, verbose=False): - self.error_msg = """ -The PET driver requires (a) a path to the results/experiment_name folder emitted by pet_train - (b) a path to an ase.io.read-able file with a prototype structure - -Other arguments to the pet.SingleStructCalculator class can be optionally -supplied in key=value form after the required arguments. - -Example: python driver.py -m pet -u -o "path/to/results/name,template.xyz,device=cuda" -""" - - super().__init__(args, verbose) - - if PETCalc is None: - raise ImportError("Couldn't load PET bindings") - - def check_arguments(self): + """ + Driver for `PET` MLIPs + The driver requires specification of the folder containing the + outputs from a PET model training, a template file that describes the chemical makeup + of the structure, and optional parameters specific for the PET architecture. + Requires the pet library + + Command-line: + i-pi-py_driver -m pet -o model_path=path_to_results/prefix,template=template.xyz,device=cuda [...] + + Parameters: + :param template: string, filename of an ASE-readable structure file + to initialize atomic number and types + :param model: string, filename of the torchscript model file + :param device: string, optional, ["cpu" | "cuda"] + """ + + def __init__(self, model_path, template, *args, **kwargs): + global PETCalc, read + + try: + from pet import SingleStructCalculator as PETCalc + + try: + from ase.io import read + except ImportError: + warning("The PET driver has an ASE dependency") + raise + except ImportError: + raise ImportError("Could not find or import the PET module") + + self.model_path = model_path + self.template = template + super().__init__(*args, **kwargs) + + def check_parameters(self): """Check the arguments required to run the driver This loads the potential and atoms template in PET """ - args = self.args - - if len(args) >= 2: - self.model_path = args[0] - self.template = args[1] - kwargs = {} - if len(args) > 2: - for arg in args[2:]: - key, value = arg.split("=") - lookup = { - "None": None, - "False": False, - "True": True, - } - - if value in lookup: - value = lookup[value] - - kwargs[key] = value - - else: - sys.exit(self.error_msg) self.template_ase = read(self.template) self.template_ase.arrays["forces"] = np.zeros_like(self.template_ase.positions) self.pet_calc = PETCalc( self.model_path, - **kwargs, + **self.kwargs, ) def __call__(self, cell, pos): diff --git a/drivers/py/pes/rascal.py b/ipi/pes/rascal.py similarity index 56% rename from drivers/py/pes/rascal.py rename to ipi/pes/rascal.py index c7ac7da31..7bef90025 100644 --- a/drivers/py/pes/rascal.py +++ b/ipi/pes/rascal.py @@ -1,45 +1,53 @@ """Interface with librascal to run machine learning potentials""" -import sys from .dummy import Dummy_driver from ipi.utils.mathtools import det_ut3x3 from ipi.utils.units import unit_to_internal, unit_to_user +from ipi.utils.messages import verbosity, warning -try: - from rascal.models.genericmd import GenericMDCalculator as RascalCalc -except: - RascalCalc = None +RascalCalc = None __DRIVER_NAME__ = "rascal" __DRIVER_CLASS__ = "Rascal_driver" -ERROR_MSG = """ -Rascal driver requires specification of a .json model file fitted with librascal, -and a template file that describes the chemical makeup of the structure. -Example: python driver.py -m rascal -u -o model.json,template.xyz -""" - class Rascal_driver(Dummy_driver): - def __init__(self, args=None, verbose=False): - super().__init__(args, verbose, error_msg=ERROR_MSG) + """ + Driver for `librascal` MLIPs + The driver requires specification of the model JSON-formated definition, + and a template file that describes the chemical makeup + of the structure. Requires the librascal library + + Command-line: + i-pi-py_driver -m rascal -o model=model.json,template=template.xyz [...] + + Parameters: + :param template: string, filename of an ASE-readable structure file + to initialize atomic number and types + :param model: string, filename of the torchscript model file + """ - if RascalCalc is None: + def __init__(self, model, template, *args, **kwargs): + global RascalCalc + warning( + "THIS PES HAS NOT BEEN TESTED FOLLOWING CONVERSION TO THE NEW PES API.", + verbosity.low, + ) + try: + from rascal.models.genericmd import GenericMDCalculator as RascalCalc + except: raise ImportError("Couldn't load librascal bindings") + self.model = model + self.template = template - def check_arguments(self): + super().__init__(*args, **kwargs) + + def check_parameters(self): """Check the arguments required to run the driver This loads the potential and atoms template in librascal """ - arglist = self.args - - if len(arglist) == 2: - self.model = arglist[0] - self.template = arglist[1] - else: - sys.exit(self.error_msg) self.rascal_calc = RascalCalc(self.model, True, self.template) diff --git a/ipi/pes/so3lr.py b/ipi/pes/so3lr.py new file mode 100644 index 000000000..c0ee083c5 --- /dev/null +++ b/ipi/pes/so3lr.py @@ -0,0 +1,37 @@ +""" An interface for the [SO3LR](https://github.com/general-molecular-simulations/so3lr) calculator """ + +from .ase import ASEDriver +from ipi.utils.messages import verbosity, warning + +So3lrCalculator = None + +__DRIVER_NAME__ = "so3lr" +__DRIVER_CLASS__ = "SO3LR_driver" + + +class SO3LR_driver(ASEDriver): + """ + SO3LR driver requires a template file that describes the chemical makeup of the structure. + + Optionally, lr_cutoff and dispersion_energy_lr_cutoff_damping can be specified. + + Example: python driver.py -m so3lr -u -o template.xyz,lr_cutoff=12,dispersion_energy_lr_cutoff_damping=2 + """ + + def __init__(self, *args, **kwargs): + warning( + "THIS PES HAS NOT BEEN TESTED FOLLOWING CONVERSION TO THE NEW PES API.", + verbosity.low, + ) + global So3lrCalculator + try: + from so3lr import So3lrCalculator + except: + raise ImportError("Couldn't load so3lr bindings") + + super().__init__(*args, **kwargs) + + def check_parameters(self): + super().check_parameters() + + self.ase_calculator = So3lrCalculator(**self.kwargs) diff --git a/drivers/py/pes/spline.py b/ipi/pes/spline.py similarity index 84% rename from drivers/py/pes/spline.py rename to ipi/pes/spline.py index eb7de4ea4..3adbd0821 100644 --- a/drivers/py/pes/spline.py +++ b/ipi/pes/spline.py @@ -6,6 +6,8 @@ from scipy import interpolate import json +from ipi.utils.messages import verbosity, warning + """Spline driver. This is not a serious interpolation, use it if you know what you are doing. """ factor_coord = 5 mass = 1836 @@ -18,21 +20,27 @@ class Spline_driver(Dummy_driver): - def __init__(self, args=None, verbose=None): - self.error_msg = """\nspline driver requires specification of filename that contains 5 columns (pos, f1,f2,f3,e) to perform 3x1D spline.\nExample: python driver.py -m spline -u -o \n""" - super(Spline_driver, self).__init__(args) + """\nspline driver requires specification of filename that contains 5 columns (pos, f1,f2,f3,e) to perform 3x1D spline.\nExample: python driver.py -m spline -u -o \n""" + + def __init__(self, data_file, *args, **kwargs): + warning( + "THIS PES HAS NOT BEEN TESTED FOLLOWING CONVERSION TO THE NEW PES API.", + verbosity.low, + ) + self.data_file = data_file + super().__init__(*args, **kwargs) self.get_spline() if friction and not SI: self.get_spline_fric() self.k = 1836 * (3800.0 / 219323.0) ** 2 - def check_arguments(self): + def check_parameters(self): """Function that checks the arguments required to run the driver""" try: - data = np.loadtxt(self.args[0]).reshape(-1, 5) + data = np.loadtxt(self.data_file).reshape(-1, 5) except ValueError: - sys.exit(self.error_msg) + sys.exit(self._error_msg) self.data = data def get_spline(self): diff --git a/drivers/py/pes/xtb.py b/ipi/pes/xtb.py similarity index 74% rename from drivers/py/pes/xtb.py rename to ipi/pes/xtb.py index 144a07c67..687c8768b 100644 --- a/drivers/py/pes/xtb.py +++ b/ipi/pes/xtb.py @@ -1,42 +1,40 @@ -""" -Interface with tblite to provide GFN1-xTB and GFN2-xTB calculators. - -Example:: - - python driver.py -m xtb -u -o '{"method": "GFN2-xTB", "numbers": [8,1,1], "periodic": false}' -""" - import numpy as np import json from ipi.utils.units import unit_to_internal, unit_to_user +from ipi.utils.messages import verbosity, warning +from .dummy import Dummy_driver -try: - import tblite.interface as tb -except ImportError: - tb = None - +tb = None __DRIVER_NAME__ = "xtb" __DRIVER_CLASS__ = "TBLiteDriver" -class TBLiteDriver(object): - """Base class providing the structure of a PES for the python driver.""" +class TBLiteDriver(Dummy_driver): + """ + Interface with tblite to provide GFN1-xTB and GFN2-xTB calculators. + + Example:: - def __init__( - self, - args="", - verbose=False, - ): - """Initialized dummy drivers""" + python driver.py -m xtb -u -o config.json + """ - if tb is None: + def __init__(self, json_input, *args, **kwargs): + warning( + "THIS PES HAS NOT BEEN TESTED FOLLOWING CONVERSION TO THE NEW PES API.", + verbosity.low, + ) + config = json.load(open(json_input)) + + global tb + try: + import tblite.interface as tb + except ImportError: raise ModuleNotFoundError( "Could not find tblite for xtb driver. Please install tblite-python with mamba" ) - config = json.loads(args) try: self.method = config["method"] self.numbers = np.asarray(config["numbers"]) @@ -45,7 +43,9 @@ def __init__( self.charge = config.get("charge") self.uhf = config.get("uhf") self.periodic = config.get("periodic") - self.verbosity = 1 if verbose else 0 + self.verbosity = 1 if self.verbose else 0 + + super().__init__(*args, **kwargs) def __call__(self, cell, pos): """ diff --git a/ipi/utils/io/inputs/__init__.py b/ipi/utils/io/inputs/__init__.py index e766bce28..aad0bbbf8 100644 --- a/ipi/utils/io/inputs/__init__.py +++ b/ipi/utils/io/inputs/__init__.py @@ -8,3 +8,37 @@ __all__ = ["io_xml"] + + +def read_value(s): + """Attempt to parse a string to int or float; fallback to string.""" + s = s.strip() + for cast in (int, float): + try: + return cast(s) + except ValueError: + continue + return s + + +def read_args_kwargs(input_str): + """ + Parses a string into positional arguments and keyword arguments. + + Args: + input_str (str): The input string containing comma-separated values and key-value pairs. + + Returns: + tuple: A tuple containing a list of positional arguments and a dictionary of keyword arguments. + """ + args = [] + kwargs = {} + tokens = input_str.split(",") + for token in tokens: + token = token.strip() + if "=" in token: + key, value = token.split("=", 1) + kwargs[key.strip()] = read_value(value) + elif len(token) > 0: + args.append(read_value(token)) + return args, kwargs diff --git a/ipi/utils/io/inputs/io_xml.py b/ipi/utils/io/inputs/io_xml.py index 7ecb2ac68..8fbc0a261 100644 --- a/ipi/utils/io/inputs/io_xml.py +++ b/ipi/utils/io/inputs/io_xml.py @@ -12,6 +12,7 @@ import numpy as np from ipi import ipi_global_settings +from . import read_value __all__ = [ "xml_node", @@ -448,7 +449,7 @@ def mystrip(data): rtuple = list(map(mystrip, s.split(key_split))) if not len(rtuple) == 2: raise ValueError("Format for a key:value format is wrong for item " + s) - rdict[rtuple[0]] = rtuple[1] + rdict[rtuple[0]] = read_value(rtuple[1]) return rdict diff --git a/ipi_tests/README.md b/ipi_tests/README.md index 97b667f3e..152d4a5ac 100644 --- a/ipi_tests/README.md +++ b/ipi_tests/README.md @@ -14,7 +14,10 @@ * To run the unitary, example and regression tests, please use i-pi/bin/i-pi-tests. For details of usage call it with "-h" option. - * In some situations it is desirable to perform regresion/examples tests only for a selected set. + * The tests can be customized to an extent by including a `test_settings.dat` file that specifies how to run the test, + mostly by describing the driver that should be used. See some of the existing files as examples. + + * In some situations it is desirable to perform regression/examples tests only for a selected set. For these cases, we also provide more flexible scripts for performing the regresion tests and testing the provided examples. See i-pi/ipi_tests/regression_tests/test_run.py and i-pi/ipi_tests/examples/test_examples.py, respectively. For details of usage call them with "-h" option. diff --git a/ipi_tests/profiling/classical_md_direct/init.xyz b/ipi_tests/profiling/classical_md_direct/init.xyz new file mode 100644 index 000000000..f2f3870f8 --- /dev/null +++ b/ipi_tests/profiling/classical_md_direct/init.xyz @@ -0,0 +1,10 @@ +8 +# CELL(abcABC): 50.0 50.0 50.0 90.00000 90.00000 90.00000 +H 0 0 0 +H 0 0 1 +H 0 0 2 +H 0 0 3 +H 0 0 4 +H 0 0 5 +H 0 0 6 +H 0 0 7 diff --git a/ipi_tests/profiling/classical_md_direct/input.xml b/ipi_tests/profiling/classical_md_direct/input.xml new file mode 100644 index 000000000..21d038b66 --- /dev/null +++ b/ipi_tests/profiling/classical_md_direct/input.xml @@ -0,0 +1,34 @@ + + + dummy + 1.00000000e-04 + + 10000 + + positions + [ step, time, conserved, temperature, kinetic_md, potential, pressure_md, volume ] + + + 18885 + + + + + + + init.xyz + [10.0, 0, 0, 0, 10.0, 0, 0, 0, 10.0] + [1.0] + 1 + + + 1 + + + False + + 0.01 + + + + diff --git a/ipi_tests/profiling/run_profiling.sh b/ipi_tests/profiling/run_profiling.sh index c475445c0..b8ae0bfb8 100755 --- a/ipi_tests/profiling/run_profiling.sh +++ b/ipi_tests/profiling/run_profiling.sh @@ -1,5 +1,5 @@ #!/bin/bash -# usage: run_profile.sh [-p] natoms [ndriver] +# usage: run_profiling.sh [-p] natoms [ndriver] # run a mock simulation using an natoms box, -p activates yappi profiling # Default value for natoms diff --git a/ipi_tests/regression_tests/tests/INSTANTON/100K_implicit_friction/simulation.instanton_FINAL_15.ener b/ipi_tests/regression_tests/tests/INSTANTON/100K_implicit_friction/simulation.instanton_FINAL_15.ener deleted file mode 100644 index 6a2a6e394..000000000 --- a/ipi_tests/regression_tests/tests/INSTANTON/100K_implicit_friction/simulation.instanton_FINAL_15.ener +++ /dev/null @@ -1,33 +0,0 @@ -#Bead Energy (eV) -0 -0.11866259790715851 -1 -0.11691012681205774 -2 -0.11342166079444242 -3 -0.1082351949410836 -4 -0.10141984639090063 -5 -0.09308898239047224 -6 -0.08341517679588735 -7 -0.0726445585426023 -8 -0.06110741669327686 -9 -0.049221487325502286 -10 -0.03748445701371601 -11 -0.026453159043353814 -12 -0.016708861462551 -13 -0.008810819030011201 -14 -0.0032433701350644724 -15 -0.0003644451312916968 -16 -0.0003644451319317277 -17 -0.0032433701369415356 -18 -0.008810819032999921 -19 -0.016708861466452396 -20 -0.026453159047914718 -21 -0.03748445701864777 -22 -0.04922148733051311 -23 -0.06110741669809458 -24 -0.07264455854700659 -25 -0.0834151767997177 -26 -0.09308898239364362 -27 -0.10141984639339816 -28 -0.10823519494296141 -29 -0.11342166079580748 -30 -0.11691012681305872 -31 -0.11866259790797011 diff --git a/ipi_tests/regression_tests/tests/INSTANTON/100K_implicit_friction/test_settings.dat b/ipi_tests/regression_tests/tests/INSTANTON/100K_implicit_friction/test_settings.dat index 42ec12ec1..0d6ab5051 100644 --- a/ipi_tests/regression_tests/tests/INSTANTON/100K_implicit_friction/test_settings.dat +++ b/ipi_tests/regression_tests/tests/INSTANTON/100K_implicit_friction/test_settings.dat @@ -1,6 +1,6 @@ driver_model DW_friction driver_code python -flags -o 500,2085,1837.36223469,0,1.5,-1.0,0,1 +flags -o 'w_b=500,v0=2085,m=1837.36223469,delta=0,eta0=1.5,eps1=-1.0,eps2=0,deltaQ=1' address localhost port 33335 socket_mode unix diff --git a/setup.py b/setup.py index bf8364962..e865e9c79 100644 --- a/setup.py +++ b/setup.py @@ -6,13 +6,6 @@ scripts = [str(p) for p in Path("bin").iterdir() if p.name != "i-pi-driver"] setup( - packages=[ - *find_packages(exclude=["ipi_tests*"]), - "ipi._driver", - "ipi._driver.pes", - ], - package_dir={ - "ipi._driver": "drivers/py", - }, + packages=[*find_packages(exclude=["ipi_tests*"])], scripts=scripts, )