Add 'addatom' action (#1092)

* Start addatom

* Init the top writer

* Modified, not stripped

* Finish initial incarnation

* Set up topology

* Enable command

* Add test save files

* If incoming top has pdb or extra amber atom info, make sure placeholder
values are added

* Functions for adding extra amber atom info

* Add test

* Add mass and charge keywords, add test

* 6.27.3. Revision bump for new 'addatom' action.

* Add manual entry for addatom.

* Disable the Jenkins intel build since the node has been offline for a
while.

* Upgrade wrapper document to lyx 2.4 as well.

Jenkinsfile

@@ -74,33 +74,33 @@ pipeline {
 
                     post { cleanup { deleteDir() } }
                 }
-                stage("Linux Intel Serial Build") {
-                    when { expression { return false } }
-                    agent {
-                        docker {
-                            image 'ambermd/cpu-build:latest'
-                            alwaysPull true
-                            label "docker && intel"
-                            // There's no way to have a docker container installed with a licensed
-                            // copy of the Intel compilers, so we need to mount it from the host
-                            // machine. This introduces the constraint that *all* of the Jenkins
-                            // slaves need to have the Intel compilers available at /opt/intel
-                            args "-v /opt/intel:/opt/intel"
-                        }
-                    }
+                //stage("Linux Intel Serial Build") {
+                //    when { expression { return false } }
+                //    agent {
+                //        docker {
+                //            image 'ambermd/cpu-build:latest'
+                //            alwaysPull true
+                //            label "docker && intel"
+                //            // There's no way to have a docker container installed with a licensed
+                //            // copy of the Intel compilers, so we need to mount it from the host
+                //            // machine. This introduces the constraint that *all* of the Jenkins
+                //            // slaves need to have the Intel compilers available at /opt/intel
+                //            args "-v /opt/intel:/opt/intel"
+                //        }
+                //    }
 
-                    environment {
-                        MKL_HOME = "/opt/intel/compilers_and_libraries/linux/mkl"
-                    }
+                //    environment {
+                //        MKL_HOME = "/opt/intel/compilers_and_libraries/linux/mkl"
+                //    }
 
-                    steps {
-                        unstash "source"
-                        sh "./configure --with-netcdf -mkl intel"
-                        sh "make -j4 install"
-                        sh "cd test && make test.showerrors"
-                    }
-                    post { cleanup { deleteDir() } }
-                }
+                //    steps {
+                //        unstash "source"
+                //        sh "./configure --with-netcdf -mkl intel"
+                //        sh "make -j4 install"
+                //        sh "cd test && make test.showerrors"
+                //    }
+                //    post { cleanup { deleteDir() } }
+                //}
                 //stage("Linux PGI serial build") {
                 //    agent {
                 //        docker {

doc/CpptrajManual.lyx

@@ -1,24 +1,26 @@
-#LyX 2.3 created this file. For more info see http://www.lyx.org/
-\lyxformat 544
+#LyX 2.4 created this file. For more info see https://www.lyx.org/
+\lyxformat 620
 \begin_document
 \begin_header
 \save_transient_properties true
 \origin unavailable
 \textclass article
 \use_default_options true
-\maintain_unincluded_children false
+\maintain_unincluded_children no
 \language english
 \language_package default
-\inputencoding auto
-\fontencoding global
+\inputencoding auto-legacy
+\fontencoding auto
 \font_roman "default" "default"
 \font_sans "default" "default"
 \font_typewriter "default" "default"
 \font_math "auto" "auto"
 \font_default_family default
 \use_non_tex_fonts false
 \font_sc false
-\font_osf false
+\font_roman_osf false
+\font_sans_osf false
+\font_typewriter_osf false
 \font_sf_scale 100 100
 \font_tt_scale 100 100
 \use_microtype false
@@ -62,7 +64,9 @@
 \suppress_date false
 \justification true
 \use_refstyle 1
+\use_formatted_ref 0
 \use_minted 0
+\use_lineno 0
 \index Index
 \shortcut idx
 \color #008000
@@ -78,11 +82,16 @@
 \papercolumns 1
 \papersides 1
 \paperpagestyle default
+\tablestyle default
 \tracking_changes false
 \output_changes false
+\change_bars false
+\postpone_fragile_content false
 \html_math_output 0
 \html_css_as_file 0
 \html_be_strict false
+\docbook_table_output 0
+\docbook_mathml_prefix 1
 \end_header
 
 \begin_body
@@ -124,6 +133,7 @@ LatexCommand tableofcontents
 \begin_inset CommandInset include
 LatexCommand input
 filename "cpptraj.lyx"
+literal "true"
 
 \end_inset