Skip to content

Commit

Permalink
Backported the fix in PR 132 to main
Browse files Browse the repository at this point in the history
  • Loading branch information
@chryswoods
chryswoods committed Dec 5, 2023
1 parent 8cf9c15 commit 032b4dd
Show file tree
Hide file tree
Showing 4 changed files with 185 additions and 89 deletions.
177 changes: 91 additions & 86 deletions doc/source/cheatsheet/openmm.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -73,91 +73,97 @@ by setting values for the ``temperature`` and ``pressure`` keys.

Available keys and allowable values are listed below.

+---------------------------+----------------------------------------------------------+
| Key | Valid values |
+===========================+==========================================================+
| com_reset_frequency | The frequency at which the ``CMMotionRemover`` acts to |
| | remove center of mass relative motion. If this is not |
| | set (the default) then center of mass motion is not |
| | removed. |
+---------------------------+----------------------------------------------------------+
| constraint | Type of constraint to use for bonds and/or angles. |
| | Valid strings are ``none``, ``h-bonds``, ``bonds``, |
| | ``h-bonds-h-angles`` and ``bonds-h-angles``. |
+---------------------------+----------------------------------------------------------+
| coulomb_power | The coulomb power parameter used by the softening |
| | potential used to soften interactions involving |
| | ghost atoms. |
+---------------------------+----------------------------------------------------------+
| cutoff | Size of the non-bonded cutoff, e.g. |
| | ``7.5*sr.units.angstrom`` |
+---------------------------+----------------------------------------------------------+
| cutoff_type | Type of cutoff, e.g. ``PARTICLE_MESH_EWALD``, ``PME``, |
| | ``NO_CUTOFF``, ``REACTION_FIELD``, ``RF``, ``EWALD`` |
+---------------------------+----------------------------------------------------------+
| cpu_pme | Boolean value, e.g. ``True`` or ``False`` as to whether |
| | or not PME should be evaluated on the CPU rather than |
| | on the GPU. |
+---------------------------+----------------------------------------------------------+
| device | Any valid OpenMM device number or device string, e.g. |
| | ``0`` would select device 0 |
+---------------------------+----------------------------------------------------------+
| dielectric | Dielectric value if a reaction field cutoff is used, |
| | e.g. ``78.0`` |
+---------------------------+----------------------------------------------------------+
| fixed | The atoms in the system that should be fixed (not moved) |
+---------------------------+----------------------------------------------------------+
| ignore_perturbations | Whether or not to ignore any perturbations and only set |
| | up a perturbable molecule as a non-perurbable molecule |
| | from only the reference state. |
+---------------------------+----------------------------------------------------------+
| integrator | The MD integrator to use, e.g. |
| | ``verlet``, ``leapfrog``, ``langevin``, |
| | ``langevin_middle``, ``nose_hoover``, |
| | ``brownian``, ``andersen`` |
+---------------------------+----------------------------------------------------------+
| friction | Friction value for the integrator, in inverse time, e.g. |
| | ``5.0 / sr.units.picosecond`` |
+---------------------------+----------------------------------------------------------+
| lambda | The λ-value at which to set up the system (assuming this |
| | contains any perturbable molecules or restraints) |
+---------------------------+----------------------------------------------------------+
| platform | Any valid OpenMM platform string, e.g. ``CUDA``, |
| | ``OpenCL``, ``Metal``, ```CPU``, ``Reference`` |
+---------------------------+----------------------------------------------------------+
| precision | Any valid OpenMM platform precision value, e.g. |
| | ``single``, ``mixed`` or ``double``. |
+---------------------------+----------------------------------------------------------+
| pressure | Any pressure value, e.g. ``1*sr.units.atm`` |
+---------------------------+----------------------------------------------------------+
| restraints | The :class:`~sire.mm.Restraints` object (or list of |
| | objects) that describe the restraints that should be |
| | added to the system. |
+---------------------------+----------------------------------------------------------+
| schedule | The :class:`~sire.cas.LambdaSchedule` to use that |
| | controls how parameters are modified with λ |
+---------------------------+----------------------------------------------------------+
| shift_delta | The shift_delta parameter to use for the softening |
| | potential used to soften interactions involving |
| | ghost atoms. |
+---------------------------+----------------------------------------------------------+
| space | Space in which the simulation should be conducted, e.g. |
| | `sr.vol.Cartesian` |
+---------------------------+----------------------------------------------------------+
| swap_end_states | Whether to swap the end states of a perturbable molecule |
| | (i.e. treat the perturbed state as the reference state |
| | and vice versa). |
+---------------------------+----------------------------------------------------------+
| temperature | Any temperature value, e.g. ``25*sr.units.celsius`` |
+---------------------------+----------------------------------------------------------+
| threads | The number of threads to use in the CPU platform |
+---------------------------+----------------------------------------------------------+
| timestep | Time between integration steps, e.g. |
| | ``2 * sr.units.femtosecond`` |
+---------------------------+----------------------------------------------------------+
| use_dispersion_correction | Whether or not to use the dispersion correction to |
| | deal with cutoff issues. This is very expensive. |
+---------------------------+----------------------------------------------------------+
+------------------------------+----------------------------------------------------------+
| Key | Valid values |
+==============================+==========================================================+
| com_reset_frequency | The frequency at which the ``CMMotionRemover`` acts to |
| | remove center of mass relative motion. If this is not |
| | set (the default) then center of mass motion is not |
| | removed. |
+------------------------------+----------------------------------------------------------+
| constraint | Type of constraint to use for bonds and/or angles. |
| | Valid strings are ``none``, ``h-bonds``, ``bonds``, |
| | ``h-bonds-h-angles`` and ``bonds-h-angles``. |
+------------------------------+----------------------------------------------------------+
| coulomb_power | The coulomb power parameter used by the softening |
| | potential used to soften interactions involving |
| | ghost atoms. |
+------------------------------+----------------------------------------------------------+
| cutoff | Size of the non-bonded cutoff, e.g. |
| | ``7.5*sr.units.angstrom`` |
+------------------------------+----------------------------------------------------------+
| cutoff_type | Type of cutoff, e.g. ``PARTICLE_MESH_EWALD``, ``PME``, |
| | ``NO_CUTOFF``, ``REACTION_FIELD``, ``RF``, ``EWALD`` |
+------------------------------+----------------------------------------------------------+
| cpu_pme | Boolean value, e.g. ``True`` or ``False`` as to whether |
| | or not PME should be evaluated on the CPU rather than |
| | on the GPU. |
+------------------------------+----------------------------------------------------------+
| device | Any valid OpenMM device number or device string, e.g. |
| | ``0`` would select device 0 |
+------------------------------+----------------------------------------------------------+
| dielectric | Dielectric value if a reaction field cutoff is used, |
| | e.g. ``78.0`` |
+------------------------------+----------------------------------------------------------+
| fixed | The atoms in the system that should be fixed (not moved) |
+------------------------------+----------------------------------------------------------+
| ignore_perturbations | Whether or not to ignore any perturbations and only set |
| | up a perturbable molecule as a non-perurbable molecule |
| | from only the reference state. |
+------------------------------+----------------------------------------------------------+
| include_constrained_energies | Whether or not to include the bond and angle energies |
| | of bonds and angles that are constrained. |
| | This defaults to ``True``, as we normally do want |
| | to calculate all of the energies of the internals, |
| | even if they are constrained. |
+------------------------------+----------------------------------------------------------+
| integrator | The MD integrator to use, e.g. |
| | ``verlet``, ``leapfrog``, ``langevin``, |
| | ``langevin_middle``, ``nose_hoover``, |
| | ``brownian``, ``andersen`` |
+------------------------------+----------------------------------------------------------+
| friction | Friction value for the integrator, in inverse time, e.g. |
| | ``5.0 / sr.units.picosecond`` |
+------------------------------+----------------------------------------------------------+
| lambda | The λ-value at which to set up the system (assuming this |
| | contains any perturbable molecules or restraints) |
+------------------------------+----------------------------------------------------------+
| platform | Any valid OpenMM platform string, e.g. ``CUDA``, |
| | ``OpenCL``, ``Metal``, ```CPU``, ``Reference`` |
+------------------------------+----------------------------------------------------------+
| precision | Any valid OpenMM platform precision value, e.g. |
| | ``single``, ``mixed`` or ``double``. |
+------------------------------+----------------------------------------------------------+
| pressure | Any pressure value, e.g. ``1*sr.units.atm`` |
+------------------------------+----------------------------------------------------------+
| restraints | The :class:`~sire.mm.Restraints` object (or list of |
| | objects) that describe the restraints that should be |
| | added to the system. |
+------------------------------+----------------------------------------------------------+
| schedule | The :class:`~sire.cas.LambdaSchedule` to use that |
| | controls how parameters are modified with λ |
+------------------------------+----------------------------------------------------------+
| shift_delta | The shift_delta parameter to use for the softening |
| | potential used to soften interactions involving |
| | ghost atoms. |
+------------------------------+----------------------------------------------------------+
| space | Space in which the simulation should be conducted, e.g. |
| | `sr.vol.Cartesian` |
+------------------------------+----------------------------------------------------------+
| swap_end_states | Whether to swap the end states of a perturbable molecule |
| | (i.e. treat the perturbed state as the reference state |
| | and vice versa). |
+------------------------------+----------------------------------------------------------+
| temperature | Any temperature value, e.g. ``25*sr.units.celsius`` |
+------------------------------+----------------------------------------------------------+
| threads | The number of threads to use in the CPU platform |
+------------------------------+----------------------------------------------------------+
| timestep | Time between integration steps, e.g. |
| | ``2 * sr.units.femtosecond`` |
+------------------------------+----------------------------------------------------------+
| use_dispersion_correction | Whether or not to use the dispersion correction to |
| | deal with cutoff issues. This is very expensive. |
+------------------------------+----------------------------------------------------------+

Higher level API
----------------
Expand Down Expand Up @@ -336,4 +342,3 @@ from files (e.g. via that property of the ``.trajectory()`` function).
The energies are saved to the ``energy_trajectory`` property of the
returned molecules, and accessible via that property or the
:func:`~sire.system.System.energy_trajectory` function.

5 changes: 5 additions & 0 deletions tests/conftest.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -150,3 +150,8 @@ def ethane_12dichloroethane():
@pytest.fixture(scope="session")
def pentane_cyclopentane():
return sr.load_test_files("pentane_cyclopentane.bss")


@pytest.fixture(scope="session")
def zero_lj_mols():
return sr.load_test_files("zero_lj.prm7", "zero_lj.rst7")
73 changes: 73 additions & 0 deletions tests/convert/test_openmm.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -285,3 +285,76 @@ def test_openmm_ignore_constrained(ala_mols):
# these two energies should be different, because
# we should be ignoring the constrained bonds and angles
assert abs(nrg2.value() - nrg1.value()) > 1.0


@pytest.mark.skipif(
"openmm" not in sr.convert.supported_formats(),
reason="openmm support is not available",
)
def test_openmm_no_zero_sigmas(zero_lj_mols):
mols = zero_lj_mols

omm = sr.convert.to(mols, "openmm",
map={"constraint": "h-bonds",
"platform": "Reference"})

from openmm import XmlSerializer

xml = XmlSerializer.serialize(omm.getSystem())

for line in xml.split("\n"):
assert 'sig="0"' not in line


@pytest.mark.skipif(
"openmm" not in sr.convert.supported_formats(),
reason="openmm support is not available",
)
def test_openmm_skipped_constrained_bonds(zero_lj_mols):
mols = zero_lj_mols

omm1 = sr.convert.to(
mols,
"openmm",
map={"constraint": "h-bonds",
"include_constrained_energies": True,
"platform": "Reference"},
)

omm2 = sr.convert.to(
mols,
"openmm",
map={"constraint": "h-bonds",
"include_constrained_energies": False,
"platform": "Reference"},
)

nrg1 = omm1.get_potential_energy().to(sr.units.kcal_per_mol)
nrg2 = omm2.get_potential_energy().to(sr.units.kcal_per_mol)

# Check the energies haven't changed
# (regression check - here are the current values)
assert nrg1 == pytest.approx(-447.44, 1e-3)
assert nrg2 == pytest.approx(-3279.87, 1e-3)

from openmm import XmlSerializer

xml1 = XmlSerializer.serialize(omm1.getSystem())
xml2 = XmlSerializer.serialize(omm2.getSystem())

assert xml1 != xml2

lines1 = xml1.split("\n")
lines2 = xml2.split("\n")

i = 0

for j in range(0, len(lines2)):
line1 = lines1[i]
line2 = lines2[j]
i += 1

while line1 != line2:
line1 = lines1[i]
assert "Bond" in line1
i += 1
Loading

0 comments on commit 032b4dd

Please sign in to comment.