diff --git a/.gitignore b/.gitignore index 6f1dfcd..20c4614 100644 --- a/.gitignore +++ b/.gitignore @@ -3,6 +3,9 @@ __pycache__/ *.py[cod] *$py.class +# VS Code +.vscode + # C extensions *.so @@ -107,5 +110,5 @@ ENV/ # In-tree generated files */_version.py -*/.DS_Store +*.DS_Store */.idea/ \ No newline at end of file diff --git a/alchemtest/lammps/__init__.py b/alchemtest/lammps/__init__.py new file mode 100644 index 0000000..470640a --- /dev/null +++ b/alchemtest/lammps/__init__.py @@ -0,0 +1,5 @@ +"""Simulation datasets in any form. + +""" + +from .access import load_benzene, load_lj_dimer diff --git a/alchemtest/lammps/access.py b/alchemtest/lammps/access.py new file mode 100644 index 0000000..53aa941 --- /dev/null +++ b/alchemtest/lammps/access.py @@ -0,0 +1,75 @@ +"""LAMMPS datasets. + +""" + +from os.path import dirname, join +from glob import glob + +from .. import Bunch + +def load_benzene(): + """Load data set of benzene in water. + + Returns + ------- + data: Bunch + Dictionary-like object, the interesting attributes are: + + - 'data' : the data files from lammps dump output + + * "mbar": Files formatted for BAR or MBAR + + * '1_coul-off': NPT removal of benzene's charges + * '2_vdw': NPT decoupling of vdw forces between benzene and water + * '3_coul-on': NVT in vacuum restoration of benzene's charges + + * "ti" + + * '1_coul-off': NPT removal of benzene's charges + * '2_vdw': NPT decoupling of vdw forces between benzene and water + * '3_coul-on': NVT in vacuum restoration of benzene's charges + + - 'DESCR': the full description of the dataset + + """ + module_path = dirname(__file__) + data = { + "mbar": { + '1_coul-off': glob(join(module_path, 'benzene/1_NPT_coul/mbar*.txt.bz2')), + '2_vdw': glob(join(module_path, 'benzene/2_NPT_vdw/mbar*.txt.bz2')), + '3_coul-on': glob(join(module_path, 'benzene/3_NVT_coul/mbar*.txt.bz2')), + }, + "ti": { + '1_coul-off': glob(join(module_path, 'benzene/1_NPT_coul/ti*.txt.bz2')), + '2_vdw': glob(join(module_path, 'benzene/2_NPT_vdw/ti*.txt.bz2')), + '3_coul-on': glob(join(module_path, 'benzene/3_NVT_coul/ti*.txt.bz2')), + } + } + + with open(join(module_path, 'benzene', 'descr.rst')) as rst_file: + fdescr = rst_file.read() + + return Bunch(data=data, + DESCR=fdescr) + + +def load_lj_dimer(): + """Load data set of LJ dimer in solvent. + + Returns + ------- + data: Bunch + Dictionary-like object, the interesting attributes are: + + - 'data' : the data files from lammps dump output + - 'DESCR': the full description of the dataset + + """ + module_path = dirname(__file__) + data = glob(join(module_path, 'lj_dimer/cross_epsilon/linear*.txt.bz2')) + + with open(join(module_path, 'lj_dimer', 'descr.rst')) as rst_file: + fdescr = rst_file.read() + + return Bunch(data=data, + DESCR=fdescr) \ No newline at end of file diff --git a/alchemtest/lammps/benzene/1_NPT_coul/mbar_charge_0.2_0.2.txt.bz2 b/alchemtest/lammps/benzene/1_NPT_coul/mbar_charge_0.2_0.2.txt.bz2 new file mode 100644 index 0000000..65b963d 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0000000..5217c0d --- /dev/null +++ b/alchemtest/lammps/benzene/descr.rst @@ -0,0 +1,36 @@ +LAMMPS: Benzene in Water +============================================== + +Benzene in water, alchemically decoupled to benzene in vacuum separated from bulk water + +Test using LAMMPS dump files turned into u_nk and dHdl dataframes that could be calculated +with MBAR or TI. + +Notes +----- +Data Set Characteristics: + :Number of Legs: 3 (Coulomb1 (NPT turn off Benzene charges), VDW (NPT), Coulomb2 (NVT turn on Benzene charges in vacuum)) + :Number of Windows: 6 for Coulomb1, 16 for VDW, 6 for Coulomb2 + :Length of Windows: 5ns + :System Size: 1668 atoms + :Temperature: 300 K + :Pressure: 1 bar + :Alchemical Pathway: vdw + coul --> vdw --> vacuum + :Experimental Hydration Free Energy: -0.90 +- 0.2 kcal/mol + :Missing Values: None + :Energy unit: kcal/mol + :Time unit: fs + :Creator: Jennifer A. Clark + :Donor: Jennifer A. Clark + :Date: Dec. 2024 + :License: `NIST `_ + :DOI: 10.18434/mds2-3637 + +This dataset was provided by @jaclark5 on +`NIST MIDAS `_ + +Experimental value sourced from [Mobley2013]_. + +.. [Mobley2013] Mobley, David L. (2013). Experimental and Calculated Small + Molecule Hydration Free Energies. UC Irvine: Department of Pharmaceutical + Sciences, UCI. 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Clark + :Donor: Jennifer A. Clark + :Date: Dec. 2024 + :License: `NIST `_ + :DOI: 10.18434/mds2-3637 + +This dataset was provided by @jaclark5 on +`NIST MIDAS `_ diff --git a/alchemtest/tests/test_lammps.py b/alchemtest/tests/test_lammps.py new file mode 100644 index 0000000..f7c8f69 --- /dev/null +++ b/alchemtest/tests/test_lammps.py @@ -0,0 +1,48 @@ +'''Tests for all the LAMMPS datasets''' +import pytest + +from alchemtest import Bunch +from alchemtest.lammps import load_benzene, load_lj_dimer + +from . import BaseDatasetTest + +# fake access to conform to expected API +def _load_benzene_mbar(): + dset = load_benzene() + return Bunch(data=dset.data['mbar'], + DESCR="Benzene example: mbar") + +def _load_benzene_ti(): + dset = load_benzene() + return Bunch(data=dset.data['ti'], + DESCR="Benzene example: ti") + +def _load_lj_dimer(): + dset = load_lj_dimer() + return Bunch(data={"data": dset.data}, + DESCR="LJ Dimer") + +class TestLAMMPS(BaseDatasetTest): + @pytest.fixture(scope="class", + params = [ + pytest.param( + (_load_benzene_mbar, + ('1_coul-off', '2_vdw', '3_coul-on'), + (36, 256, 36)), + id="complex" + ), + pytest.param( + (_load_benzene_ti, + ('1_coul-off', '2_vdw', '3_coul-on'), + (6, 16, 6)), + id="complex" + ), + pytest.param( + (_load_lj_dimer, + ('data', ), + (11, )), + id="complex" + ), + ]) + def dataset(self, request): + return super(TestLAMMPS, self).dataset(request) diff --git a/docs/conf.py b/docs/conf.py index 936c703..65ef262 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -72,7 +72,7 @@ # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. -language = None +language = "en" # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. @@ -170,5 +170,5 @@ # -- Extension configuration ------------------------------------------------- -intersphinx_mapping = {'https://docs.python.org/': None, +intersphinx_mapping = {'python': ('https://docs.python.org/3', None), 'alchemlyb': ('https://alchemlyb.readthedocs.io/en/latest/', None)} \ No newline at end of file diff --git a/docs/contributing.rst b/docs/contributing.rst index f88009c..8db1cbf 100644 --- a/docs/contributing.rst +++ b/docs/contributing.rst @@ -127,13 +127,17 @@ Process (possibly inside another dictionary). It should be possible to work with your dataset as shown under :ref:`usage`. - Try building the documentation with + Try building the documentation in the alchemtest/docs directory with .. code-block:: bash - python setup.py build_sphinx + make html - and look at the docs in :file:`build/sphinx/html/index.html`. + and look at the docs from the same directory with + + .. code-block:: bash + + open _build/html/index.html Check that your documentation is visible. If not, it's possible that another page needs to be added to the docs — just move ahead @@ -166,6 +170,9 @@ Process .. _`alchemtest/gmx`: https://github.com/alchemistry/alchemtest/tree/master/alchemtest/gmx +.. _`alchemtest/lammps`: + https://github.com/alchemistry/alchemtest/tree/master/alchemtest/lammps + .. _`alchemtest/namd`: https://github.com/alchemistry/alchemtest/tree/master/alchemtest/namd diff --git a/docs/index.rst b/docs/index.rst index b8fe37c..35405d6 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -69,9 +69,10 @@ suite it may contain bugs. Please raise any issues or questions in the :maxdepth: 1 :caption: Datasets - gmx amber - namd + gmx gomc + lammps + namd generic diff --git a/docs/lammps.rst b/docs/lammps.rst new file mode 100644 index 0000000..22d0724 --- /dev/null +++ b/docs/lammps.rst @@ -0,0 +1,39 @@ +.. _lammps-datasets: + +================ +LAMMPS datasets +================ +.. automodule:: alchemtest.lammps + +The :mod:`alchemtest.lammps` module features datasets generated using the +`LAMMPS `_ molecular dynamics engine. They +can be accessed using the following accessor functions: + +.. currentmodule:: alchemtest.lammps + +.. autosummary:: + + load_benzene + load_lj_dimer + + +----------------- +Simple TI and FEP +----------------- + +The data sets contain derivatives of the Hamiltonian (TI) and free +energy perturbation (FEP) data suitable for processing with FEP +estimators as well as BAR/MBAR. Individual :math:`\lambda` windows +were run independently. + + +.. _lammps_benzene: +.. include:: ../alchemtest/lammps/benzene/descr.rst + +.. autofunction:: alchemtest.lammps.load_benzene + +.. _lammps_lj_dimer: +.. include:: ../alchemtest/lammps/lj_dimer/descr.rst + +.. autofunction:: alchemtest.lammps.load_lj_dimer + \ No newline at end of file