Merge pull request #50 from OpenBioSim/fix_45-48_main

Backport fixes from PR #49

doc/source/tutorials/hydration_freenrg.rst

@@ -99,12 +99,25 @@ dynamics engine called SOMD. (This is a wrapper around the excellent
 `OpenMM <https://openmm.org>`__ package and is the default engine if no other
 packages are present.)
 
+>>> protocol = BSS.Protocol.FreeEnergyProduction()
+>>> free_somd = BSS.FreeEnergy.Relative(solvated, protocol, engine="somd", work_dir="freenrg_somd/free")
+>>> vac_somd = BSS.FreeEnergy.Relative(merged.toSystem(), protocol, engine="somd", work_dir="freenrg_somd/vacuum")
+
 .. note ::
 
- It's possible to use a different protocol or molecular dynamics engine for each leg.
+ For GROMACS, you can use :data:`BioSimSpace.Protocol.FreeEnergyMinimisation` and
+ :data:`BioSimSpace.Protocol.FreeEnergyEquilibration` to minimise and equilibrate at each
+ :math:`{\lambda}` value prior to setting up to the production run above. For SOMD this
+ isn't possible, so you can either use GROMACS to prepare production input for each window,
+ or use the regular :data:`BioSimSpace.Protocol.Minimisation` and
+ :data:`BioSimSpace.Protocol.Equilibration` protocols to minimise and equilibrate
+ the :math:`{\lambda=0}` and :math:`{\lambda=1}` states only using any supported
+ engine from :data:`BioSimSpace.Process`.
 
->>> free_somd = BSS.FreeEnergy.Relative(solvated, protocol, engine="somd", work_dir="freenrg_somd/free")
->>> vac_somd = BSS.FreeEnergy.Relative(merged.toSystem(), protocol, engine="somd", work_dir="freenrg_somd/vacuum")
+.. note ::
+
+ It's possible to use a different protocol or molecular dynamics engine for each leg,
+ e.g. if you want to use a different :math:`{\lambda}` schedule.
 
 When complete, BioSimSpace will have set up a folder hierarchy containing
 everything that is needed to run the hydration free energy calculation

python/BioSimSpace/FreeEnergy/_relative.py

@@ -95,6 +95,8 @@ def __init__(
  setup_only=False,
  ignore_warnings=False,
  show_errors=True,
+ extra_options={},
+ extra_lines=[],
  property_map={},
  ):
  """
@@ -139,6 +141,13 @@ def __init__(
  run file. This option is specific to GROMACS and will be ignored
  when a different molecular dynamics engine is chosen.
 
+ extra_options : dict
+ A dictionary containing extra options. Overrides the defaults generated
+ by the protocol.
+
+ extra_lines : [str]
+ A list of extra lines to put at the end of the configuration file.
+
  property_map : dict
  A dictionary that maps system "properties" to their user defined
  values. This allows the user to refer to properties with their
@@ -249,6 +258,23 @@ def __init__(
  raise ValueError("'show_errors' must be of type 'bool.")
  self._show_errors = show_errors
 
+ # Check the extra options.
+ if not isinstance(extra_options, dict):
+ raise TypeError("'extra_options' must be of type 'dict'.")
+ else:
+ keys = extra_options.keys()
+ if not all(isinstance(k, str) for k in keys):
+ raise TypeError("Keys of 'extra_options' must be of type 'str'.")
+ self._extra_options = extra_options
+
+ # Check the extra lines.
+ if not isinstance(extra_lines, list):
+ raise TypeError("'extra_lines' must be of type 'list'.")
+ else:
+ if not all(isinstance(line, str) for line in extra_lines):
+ raise TypeError("Lines in 'extra_lines' must be of type 'str'.")
+ self._extra_lines = extra_lines
+
  # Check that the map is valid.
  if not isinstance(property_map, dict):
  raise TypeError("'property_map' must be of type 'dict'")
@@ -856,6 +882,8 @@ def _initialise_runner(self, system):
  self._protocol,
  platform=platform,
  work_dir=first_dir,
+ extra_options=self._extra_options,
+ extra_lines=self._extra_lines,
  property_map=self._property_map,
  )
  if self._setup_only:
@@ -871,6 +899,9 @@ def _initialise_runner(self, system):
  work_dir=first_dir,
  ignore_warnings=self._ignore_warnings,
  show_errors=self._show_errors,
+ extra_options=self._extra_options,
+ extra_lines=self._extra_lines,
+ property_map=self._property_map,
  )
  if self._setup_only:
  del first_process

python/BioSimSpace/_Config/_somd.py

@@ -232,8 +232,11 @@ def createConfig(self, extra_options={}, extra_lines=[]):
  % self._protocol.getStartTemperature().kelvin().value()
  )
 
- # Friction coefficient (1 / ps).
- protocol_dict["inverse friction"] = "{:.5f}".format(
+ # Friction coefficient (1 / ps). Note that the unit is written
+ # to the configuration file as "picosecond". This is because SOMD
+ # applies the value to OpenMM without inverting it, so has things the
+ # wrong way round, i.e. it uses the inverse friction as the friction.
+ protocol_dict["inverse friction"] = "{:.5f} picosecond".format(
  1 / self._protocol.getThermostatTimeConstant().picoseconds().value()
  )
 

test/Process/test_somd.py

@@ -172,10 +172,8 @@ def run_process(system, protocol):
  )
  res = False
 
- return not res
-
  # Make sure the process didn't error.
- assert not process.isError()
+ assert not res
 
  # Make sure that we get a molecular system back.
  assert process.getSystem() is not None

test/Sandpit/Exscientia/Process/test_somd.py

@@ -155,10 +155,8 @@ def run_process(system, protocol):
  )
  res = False
 
- return not res
-
  # Make sure the process didn't error.
- assert not process.isError()
+ assert not res
 
  # Make sure that we get a molecular system back.
  assert process.getSystem() is not None