From f44fcb58f3dfe013af5fc747c3d21755d9436226 Mon Sep 17 00:00:00 2001 From: Zhiyi Wu Date: Sun, 31 Mar 2024 13:18:35 +0100 Subject: [PATCH 1/2] update cocs --- docs/estimators-fep.rst | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/docs/estimators-fep.rst b/docs/estimators-fep.rst index d633f7a1..b97f59b6 100644 --- a/docs/estimators-fep.rst +++ b/docs/estimators-fep.rst @@ -34,7 +34,13 @@ The :meth:`~alchemlyb.estimators.MBAR.fit` method is used to perform the free en >>> mbar_vdw = MBAR().fit(u_nk_vdw) The sum of the endpoint free energy differences will be the free energy of solvation for benzene in water. -The free energy differences (in units of :math:`k_B T`) between each :math:`\lambda` window can be accessed via the ``delta_f_`` attribute:: +The free energy differences (in units of :math:`k_B T`) between each :math:`\lambda` window can be accessed via the ``delta_f_`` attribute. + +The elements of the resulting matrix `delta_f_` represent the free energy differences between different lambda windows. Specifically, `delta_f_[i, j]` represents the free energy difference between lambda window `j` and lambda window `i`. This matrix can be utilized to obtain the desired free energy differences for various states. + +For instance, to obtain the free energy difference between the lambda values of 0 and 1, you can directly access `delta_f_.loc[0.00, 1.00]`. + +Additionally, the errors on these differences are accessible via the ``d_delta_f_`` attribute. >>> mbar_coul.delta_f_ 0.00 0.25 0.50 0.75 1.00 From 8ce070f7b0af05d522267ecdab1955c38bb35c3f Mon Sep 17 00:00:00 2001 From: Zhiyi Wu Date: Mon, 1 Apr 2024 19:59:30 +0100 Subject: [PATCH 2/2] mono-spaced --- docs/estimators-fep.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/estimators-fep.rst b/docs/estimators-fep.rst index b97f59b6..0c70586f 100644 --- a/docs/estimators-fep.rst +++ b/docs/estimators-fep.rst @@ -36,9 +36,9 @@ The :meth:`~alchemlyb.estimators.MBAR.fit` method is used to perform the free en The sum of the endpoint free energy differences will be the free energy of solvation for benzene in water. The free energy differences (in units of :math:`k_B T`) between each :math:`\lambda` window can be accessed via the ``delta_f_`` attribute. -The elements of the resulting matrix `delta_f_` represent the free energy differences between different lambda windows. Specifically, `delta_f_[i, j]` represents the free energy difference between lambda window `j` and lambda window `i`. This matrix can be utilized to obtain the desired free energy differences for various states. +The elements of the resulting matrix ``delta_f_`` represent the free energy differences between different lambda windows. Specifically, ``delta_f_[i, j]`` represents the free energy difference between lambda window ``j`` and lambda window ``i``. This matrix can be utilized to obtain the desired free energy differences for various states. -For instance, to obtain the free energy difference between the lambda values of 0 and 1, you can directly access `delta_f_.loc[0.00, 1.00]`. +For instance, to obtain the free energy difference between the lambda values of 0 and 1, you can directly access ``delta_f_.loc[0.00, 1.00]``. Additionally, the errors on these differences are accessible via the ``d_delta_f_`` attribute.