properly integrate into build system and docs

doc/src/Commands_compute.rst

@@ -63,6 +63,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`event/displace <compute_event_displace>`
    * :doc:`fabric <compute_fabric>`
    * :doc:`fep <compute_fep>`
+   * :doc:`fep/ta <compute_fep_ta>`
    * :doc:`force/tally <compute_tally>`
    * :doc:`fragment/atom <compute_cluster_atom>`
    * :doc:`global/atom <compute_global_atom>`

doc/src/compute.rst

@@ -208,7 +208,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` - rotational energy for each spherical particle
 * :doc:`event/displace <compute_event_displace>` - detect event on atom displacement
 * :doc:`fabric <compute_fabric>` - calculates fabric tensors from pair interactions
-* :doc:`fep <compute_fep>` -
+* :doc:`fep <compute_fep>` - compute free energies for alchemical transformation from perturbation theory
+* :doc:`fep/ta <compute_fep_ta>` - compute free energies for a test area perturbation
 * :doc:`force/tally <compute_tally>` - force between two groups of atoms via the tally callback mechanism
 * :doc:`fragment/atom <compute_cluster_atom>` - fragment ID for each atom
 * :doc:`global/atom <compute_global_atom>` -

doc/src/compute_fep_ta.rst

@@ -33,6 +33,7 @@ Examples
 
 Description
 """""""""""
+
 Define a computation that calculates the change in the free energy due
 to a test-area (TA) perturbation :ref:`(Gloor) <Gloor>`. The test-area
 approach can be used to determine the interfacial tension of the system
@@ -43,9 +44,9 @@ in a single simulation:
    \gamma = \lim_{\Delta \mathcal{A} \to 0} \left( \frac{\Delta A_{0 \to 1 }}{\Delta \mathcal{A}}\right)_{N,V,T}
    = - \frac{kT}{\Delta \mathcal{A}} \ln \left< \exp(-(U_1 - U_0)/kT) \right>_0
 
-During the perturbation, both axes of *plane* are scaled by multiplying :math:`\sqrt{scale\_factor}`,
+During the perturbation, both axes of *plane* are scaled by multiplying
-while the other axis divided by *scale_factor* such that the overall
+:math:`\sqrt{scale\_factor}`, while the other axis divided by
-volume of the system is maintained.
+*scale_factor* such that the overall volume of the system is maintained.
 
 The *tail* keyword controls the calculation of the tail correction to
 "van der Waals" pair energies beyond the cutoff, if this has been
@@ -59,22 +60,25 @@ Output info
 """""""""""
 
 This compute calculates a global vector of length 3 which contains the
-energy difference ( :math:`U_1-U_0` ) as c_ID[1], the
+energy difference ( :math:`U_1-U_0` ) as c_ID[1], the Boltzmann factor
-Boltzmann factor :math:`\exp(-(U_1-U_0)/kT)`, as c_ID[2] and the
+:math:`\exp(-(U_1-U_0)/kT)`, as c_ID[2] and the change in the *plane*
-change in the *plane* area :math:`\Delta \mathcal{A}` as c_ID[3]. :math:`U_1` is the
+area :math:`\Delta \mathcal{A}` as c_ID[3]. :math:`U_1` is the potential
-potential energy of the perturbed state and
+energy of the perturbed state and :math:`U_0` is the potential energy of
-:math:`U_0` is the potential energy of the reference state.
+the reference state.  The energies include kspace terms if these are
-The energies include kspace terms if these are used in the simulation.
+used in the simulation.
 
 These output results can be used by any command that uses a global
-scalar or vector from a compute as input.  See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+scalar or vector from a compute as input.  See the :doc:`Howto output
-options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`.
+<Howto_output>` page for an overview of LAMMPS output options. For
+example, the computed values can be averaged using :doc:`fix ave/time
+<fix_ave_time>`.
 
 Restrictions
 """"""""""""
 
-This compute is distributed as the FEP package.  It is only
+This compute is distributed as the FEP package.  It is only enabled if
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/utils/sphinx-config/false_positives.txt

@@ -1177,6 +1177,7 @@ Gladky
 gld
 gle
 globbing
+Gloor
 Glosli
 Glotzer
 gmail
@@ -1425,6 +1426,7 @@ interal
 interatomic
 Interatomic
 interconvert
+interfacial
 interial
 interlayer
 intermolecular

src/.gitignore

@@ -460,6 +460,8 @@
 /compute_fabric.h
 /compute_fep.cpp
 /compute_fep.h
+/compute_fep_ta.cpp
+/compute_fep_ta.h
 /compute_force_tally.cpp
 /compute_force_tally.h
 /compute_gyration_shape.cpp

src/FEP/Install.sh

@@ -30,6 +30,8 @@ action () {
 
 action compute_fep.cpp
 action compute_fep.h
+action compute_fep_ta.cpp
+action compute_fep_ta.h
 action fix_adapt_fep.cpp
 action fix_adapt_fep.h
 action pair_coul_cut_soft.cpp