diff --git a/doc/source/tutorial/part06/02_alchemical_dynamics.rst b/doc/source/tutorial/part06/02_alchemical_dynamics.rst index 52c4861ab..39e309e14 100644 --- a/doc/source/tutorial/part06/02_alchemical_dynamics.rst +++ b/doc/source/tutorial/part06/02_alchemical_dynamics.rst @@ -214,7 +214,7 @@ a :class:`sire.cas.LambdaSchedule`. You can get the λ-schedule used by the dynamics simulation using the :func:`~sire.mol.Dynamics.lambda_schedule` function, e.g. ->>> s = d.lambda_schedule() +>>> s = d.get_schedule() >>> print(s) LambdaSchedule( morph: λ * final + initial * (-λ + 1) @@ -224,13 +224,13 @@ You can plot how this schedule would morph the perturbable properties using the :func:`~sire.cas.LambdaSchedule.plot` function, e.g. >>> df = get_lever_values(initial=2.0, final=3.0) ->>> df.plot() +>>> df.plot(subplots=True) .. image:: images/06_02_01.jpg :alt: View of the default λ-schedule This shows how the different levers available in this schedule would morph -a hyperthetical parameter that has an ``initial`` value of ``2.0`` and a +a hypothetical parameter that has an ``initial`` value of ``2.0`` and a ``final`` value of ``3.0``. In this case the levers are all identical, so would change the parameter @@ -249,7 +249,7 @@ This shows that in the default ``morph`` stage of this schedule, we will scale the ``charge`` parameters by λ^2, while all other parameters (the default) will scale using λ. We can plot the result of this using; ->>> s.get_lever_values(initial=2.0, final=3.0).plot() +>>> s.get_lever_values(initial=2.0, final=3.0).plot(subplots=True) .. image:: images/06_02_02.jpg :alt: View of the λ-schedule where charge is scaled by λ^2 @@ -276,10 +276,10 @@ LambdaSchedule( charge: final * (-λ + 1) ) -Again, it is worth plotting the impact of this schedule on a hyperthetical +Again, it is worth plotting the impact of this schedule on a hypothetical parameter. ->>> s.get_lever_values(initial=2.0, final=3.0).plot() +>>> s.get_lever_values(initial=2.0, final=3.0).plot(subplots=True) .. image:: images/06_02_03.jpg :alt: View of the λ-schedule where charge is scaled in a second stage to zero. @@ -331,23 +331,15 @@ the charge lever from γ times the ``final`` value to the full ``final`` value. It also scales the charge lever in the ``morph`` stage by γ, which is set to 0.2 for all stages. -We can see how this would affect a hyperthetical parameter that goes +We can see how this would affect a hypothetical parameter that goes from an ``initial`` value of 2.0 to a ``final`` value of 3.0 via ->>> s.get_lever_values(initial=2.0, final=3.0).plot() +>>> s.get_lever_values(initial=2.0, final=3.0).plot(subplots=True) .. image:: images/06_02_04.jpg :alt: View of the λ-schedule that sandwiches a standard morph stage between two stages that scale the charge lever. -.. note:: - - Schedules constructed outside of the dynamics simulation do not have - the full set of levers (e.g. torsion_k, dih_scale etc) as - levers are only added as they are needed (hence why only - ``default`` and ``charge`` are shown here). The additional levers - are added when the schedule is added to the simulation. - Once you have created your schedule you can add it via the :meth:`~sire.mol.Dynamics.set_schedule` function of the :class:`~sire.mol.Dynamics` object, e.g. diff --git a/doc/source/tutorial/part06/images/06_02_01.jpg b/doc/source/tutorial/part06/images/06_02_01.jpg index 8674ec7aa..461cb16eb 100644 Binary files a/doc/source/tutorial/part06/images/06_02_01.jpg and b/doc/source/tutorial/part06/images/06_02_01.jpg differ diff --git a/doc/source/tutorial/part06/images/06_02_02.jpg b/doc/source/tutorial/part06/images/06_02_02.jpg index 5618f084b..1198cde9e 100644 Binary files a/doc/source/tutorial/part06/images/06_02_02.jpg and b/doc/source/tutorial/part06/images/06_02_02.jpg differ diff --git a/doc/source/tutorial/part06/images/06_02_03.jpg b/doc/source/tutorial/part06/images/06_02_03.jpg index 44694b4c6..fe39f9ab0 100644 Binary files a/doc/source/tutorial/part06/images/06_02_03.jpg and b/doc/source/tutorial/part06/images/06_02_03.jpg differ diff --git a/doc/source/tutorial/part06/images/06_02_04.jpg b/doc/source/tutorial/part06/images/06_02_04.jpg index 56af4e349..e7b0348c3 100644 Binary files a/doc/source/tutorial/part06/images/06_02_04.jpg and b/doc/source/tutorial/part06/images/06_02_04.jpg differ