Add 'openmm' keyword to 'energy' action (#1042)

* Update for precision

* Add openmm keyword to energy action, but keep it hidden for now

* Reorder the terms in esander output so they match energy output for
easier comparisons

* Put the new esander term ordering behind CPPTRAJ_ESANDER_ENERGY_ORDER
define for better backwards compatibility.

* Add new ordering option for test saves

* Add openmm and related keywords to energy help

* Add the 'name' keyword to help.

* Update manual emin entry, add name keyword. Add 'openmm' keyword to
energy manual entry.

* Add a tolerance

* 6.20.2. Revision bump for adding 'openmm' keyword to 'energy' action.

* Try to fix python build by using setup-python@v4

* Try to fix python environment

* Try to fix the python CI install

---------

Co-authored-by: Daniel R. Roe <[email protected]>

.github/workflows/merge-gate.yml

@@ -139,7 +139,7 @@ jobs:
         sudo apt-get install cmake-data cmake    
     - uses: actions/checkout@v3
     - name: Set up Python 3.8
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: 3.8
     - name: Add conda to system path
@@ -148,7 +148,7 @@ jobs:
         echo $CONDA/bin >> $GITHUB_PATH
     - name: Install conda packages
       run: |
-        conda env update --file devtools/ci/environment.yml --name base
+        conda install setuptools cython numpy pytest mock curl 
     - name: Install cpptraj
       run: |
         export PATH=$HOME/bin:${PATH}

devtools/ci/environment.yml

@@ -1,10 +1,10 @@
 channels:
-    - conda-forge
+    - defaults 
 dependencies:
-    - netcdf4
-    - pyflakes
+    - python=3.8
     - numpy
-    - cython
-    - parmed
-    - pytest
     - mock
+    - pytest
+    - cython
+    - setuptools
+    - curl 

doc/cpptraj.lyx

@@ -6744,14 +6744,21 @@ reference "subsec:cpptraj_createcrd"
 
 \begin_layout Subsection
 emin
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-emin"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout LyX-Code
 emin crdset <name> [trajoutname <name>] [rmstol <tol>] [nsteps <#>]
 \end_layout
 
 \begin_layout LyX-Code
- 	[<mask>] [frame <#>] [dx0 <step0>] [out <file>]
+ 	[<mask>] [frame <#>] [dx0 <step0>] [out <file>] [name <setname>]
 \end_layout
 
 \begin_layout LyX-Code
@@ -6819,6 +6826,14 @@ crdset
 <file>] File to write energies to.
 \end_layout
 
+\begin_layout Description
+[name
+\begin_inset space ~
+\end_inset
+
+<setname>] If specified, create an energy per step data set.
+\end_layout
+
 \begin_layout Description
 [nonbond] If specified, use simple nonbonded potential term in additon to
  bonded terms.
@@ -6841,9 +6856,61 @@ cut
 <cutoff> Set nonbonded interaction cutoff in Ang.
  (electrostatics and vdW).
  Default 8.0.
+\end_layout
+
+\begin_layout Description
+cutee
+\begin_inset space ~
+\end_inset
+
+<cutoff> Set electrostatics interaction cutoff in Ang.
 
 \end_layout
 
+\begin_layout Description
+cutnb
+\begin_inset space ~
+\end_inset
+
+<cutoff> Set vdW interaction cutoff in Ang.
+
+\end_layout
+
+\begin_layout Description
+scaleee
+\begin_inset space ~
+\end_inset
+
+<factor> Scaling factor to multiply 1-4 electrostatics interactions by.
+
+\end_layout
+
+\begin_layout Description
+scalenb
+\begin_inset space ~
+\end_inset
+
+<factor> Scaling factor to multiply 1-4 vdW interactions by.
+\end_layout
+
+\begin_layout Description
+shake
+\begin_inset space ~
+\end_inset
+
+<type> Use SHAKE constraints of <type>:
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+'hydrogen' Constrain bonds to hydrogen.
+\end_layout
+
+\begin_layout Description
+'all' Constrain all bonds.
+\end_layout
+
+\end_deeper
 \begin_layout Description
 nexclude
 \begin_inset space ~
@@ -6853,6 +6920,22 @@ nexclude
  Default 4.
 \end_layout
 
+\begin_layout Description
+qfac
+\begin_inset space ~
+\end_inset
+
+<factor> Factor to use in electrostatic calculation.
+\end_layout
+
+\begin_layout Standard
+DataSets Created
+\end_layout
+
+\begin_layout Description
+<setname>[Energy] Total energy at each minimization step.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 THIS COMMAND IS STILL IN DEVELOPMENT AS OF VERSION 5.0.2.
@@ -25467,7 +25550,7 @@ energy
 \end_layout
 
 \begin_layout LyX-Code
-energy [<name>] [<mask1>] [out <filename>] [nobondstoh]
+energy [<name>] [<mask1>] [out <filename>] [nobondstoh] [openmm [<mdopts>]]
 \end_layout
 
 \begin_layout LyX-Code
@@ -25545,6 +25628,24 @@ energy [<name>] [<mask1>] [out <filename>] [nobondstoh]
 [nobondstoh] Skip calculating the energy of bonds to hydrogen.
 \end_layout
 
+\begin_layout Description
+[openmm] If specified and CPPTRAJ is compiled with OpenMM support, use OpenMM
+ to calculate energy.
+ Note this will only calculate total energy; any keywords pertaining to
+ individual energy components are not available.
+ For a list of potential options that can be used with 'openmm', see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-emin"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+.
+\end_layout
+
 \begin_layout Description
 [bond] Calculate bond energy.
 \end_layout