Recognize Drude particles, improve handling of lone pairs (#1099)

* Start reading lone pairs * Add check for zero total mass when using mass weighting for distance * Check for zero mass in masks for angle/dihedral calcs * Read and store lone pairs * Read the lone pair atoms * Add bonds from lone pair info * Prefer https, more portable * Check for zero mass last to preserve backwards compat. as much as possible. * Add Drude element. Add support for detecting Drude particles from charmm PSF * Add geom keyword to vector, check for zero mass in masks * Hide some debug info * Version 6.29.0. Minor version bump for recognition of Drude particles and checks for zero mass in distance/angle/dihedral/vector * Add bondparminfo command * Add angle * If adding a duplicate bond, if the existing bond has no parameter but there is a parameter being passed in, use the passed in parameter. * Add some defaults for lone pair bonds * Save dihedrals. Not sure if saving torsion in phase is ok for lone pairs... * Add 'debye' keyword to report 'vector dipole' units as Debye * Add drude versions of ala3 * Add Drude PSF read test * Fix help * Document bondparminfo * Document vector geom and debye * Add old Atom constructor back for pytraj * Increase tag size by 1 for storing null for sscanf("%10s") * Add PDF versions of the manual and dev guide. * Disable automatic build of the manual until lyx on Jenkins is updated. * Change documentation URLs to GitHub for now until Jenkins is updated.
Amber-MD · Aug 29, 2024 · 6666588 · 6666588
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diff --git a/Jenkinsfile b/Jenkinsfile
@@ -191,56 +191,56 @@ pipeline {
             }
         }
 
-        stage("Post-test steps") {
-            parallel {
-                stage("Publish the manual") {
-                    stages {
-                        stage("Build the manual") {
-                            agent {
-                                docker {
-                                    image 'ambermd/lyx:latest'
-                                    alwaysPull true
-                                }
-                            }
-
-                            steps {
-                                unstash "source"
-                                sh """#!/bin/sh -ex
-                                    make docs
-                                    cd doc
-                                    lyx -batch --export pdf2 CpptrajManual.lyx
-                                    lyx -batch --export pdf2 CpptrajDevelopmentGuide.lyx
-                                """
-                                stash includes: "doc/**", name: "documentation"
-                            }
-
-                            post { cleanup { deleteDir() } }
-                        }
-                        stage("Publish the manual") {
-                            agent { label 'linux' }
-
-                            steps {
-                                unstash 'documentation'
-                                // Eventually it would be nice to do something better than simply archive
-                                // and make the artifacts available from Jenkins.
-                                archiveArtifacts 'doc/CpptrajManual.pdf,doc/CpptrajDevelopmentGuide.pdf'
-                                // It would be nice to get this in a better place, but for now this
-                                // will suffice.
-                                publishHTML([
-                                    allowMissing: false,
-                                    alwaysLinkToLastBuild: false,
-                                    keepAll: false,
-                                    reportDir: 'doc/html',
-                                    reportFiles: 'index.html',
-                                    reportName: 'Doxygen Documentation',
-                                    reportTitles: ''])
-                            }
-
-                            post { cleanup { deleteDir() } }
-                        }
-                    }
-                }
-            }
-        }
+        //stage("Post-test steps") {
+        //    parallel {
+        //        stage("Publish the manual") {
+        //            stages {
+        //                stage("Build the manual") {
+        //                    agent {
+        //                        docker {
+        //                            image 'ambermd/lyx:latest'
+        //                            alwaysPull true
+        //                        }
+        //                    }
+
+        //                    steps {
+        //                        unstash "source"
+        //                        sh """#!/bin/sh -ex
+        //                            make docs
+        //                            cd doc
+        //                            lyx -batch --export pdf2 CpptrajManual.lyx
+        //                            lyx -batch --export pdf2 CpptrajDevelopmentGuide.lyx
+        //                        """
+        //                        stash includes: "doc/**", name: "documentation"
+        //                    }
+
+        //                    post { cleanup { deleteDir() } }
+        //                }
+        //                stage("Publish the manual") {
+        //                    agent { label 'linux' }
+
+        //                    steps {
+        //                        unstash 'documentation'
+        //                        // Eventually it would be nice to do something better than simply archive
+        //                        // and make the artifacts available from Jenkins.
+        //                        archiveArtifacts 'doc/CpptrajManual.pdf,doc/CpptrajDevelopmentGuide.pdf'
+        //                        // It would be nice to get this in a better place, but for now this
+        //                        // will suffice.
+        //                        publishHTML([
+        //                            allowMissing: false,
+        //                            alwaysLinkToLastBuild: false,
+        //                            keepAll: false,
+        //                            reportDir: 'doc/html',
+        //                            reportFiles: 'index.html',
+        //                            reportName: 'Doxygen Documentation',
+        //                            reportTitles: ''])
+        //                    }
+
+        //                    post { cleanup { deleteDir() } }
+        //                }
+        //            }
+        //        }
+        //    }
+        //}
     }
 }
diff --git a/README.md b/README.md
@@ -53,17 +53,14 @@ specified in the file LICENSE.
 Documentation
 =============
   The `/doc` subdirectory contains PDF and LyX versions of the CPPTRAJ manual.
-The latest version of the manual is compiled each time new code is merged
-and is available for download
-[here.](https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/master/lastSuccessfulBuild/artifact/doc/CpptrajManual.pdf)
+The latest version of the manual is available for download
+[here.](https://raw.githubusercontent.com/Amber-MD/cpptraj/master/doc/CpptrajManual.pdf)
 An HTML version can be found [here](https://amber-md.github.io/cpptraj/). There
 is also limited help for commands in interactive mode via `help [<command>]`;
 `help` with no arguments lists all known commands.
 
-  Code documentation generated by doxygen are available
-[here.](https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/PR-773/Doxygen_20Documentation/)
-You can generate the documentation yourself with the command `make docs`. A
-limited developers guide is available [here](https://jenkins.jasonswails.com/job/amber-github/job/cpptraj/job/master/lastSuccessfulBuild/artifact/doc/CpptrajDevelopmentGuide.pdf)
+  Code documentation generated by Doxygen can be generated with the command `make docs`. A
+limited developers guide is available [here](https://raw.githubusercontent.com/Amber-MD/cpptraj/master/doc/CpptrajDevelopmentGuide.pdf)
 and limited HTML-formatted documentation is available
 [here](https://amber-md.github.io/cpptraj/).
 

diff --git a/configure b/configure
@@ -168,7 +168,7 @@ PNETCDF_OPTS='--disable-fortran --disable-cxx'
 
 FFTW_SRCTAR='fftw-3.3.9.tar.gz'
 FFTW_SRCDIR='fftw-3.3.9'
-FFTW_URL="ftp://ftp.fftw.org/pub/fftw/$FFTW_SRCTAR"
+FFTW_URL="https://fftw.org/pub/fftw/$FFTW_SRCTAR"
 FFTW_OPTS='--enable-threads --with-combined-threads --with-pic --disable-fortran'
 
 # ----- Variables for downloading MPI ------------

diff --git a/doc/CpptrajDevelopmentGuide.pdf b/doc/CpptrajDevelopmentGuide.pdf
diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
@@ -14247,7 +14247,7 @@ The following topology related commands are available:
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="22" columns="2">
+<lyxtabular version="3" rows="23" columns="2">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top">
 <column alignment="center" valignment="top">
@@ -14345,6 +14345,26 @@ Print bond info for selected atoms.
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
+\begin_layout Plain Layout
+bondparminfo
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Print the bond parameter table.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
 \begin_layout Plain Layout
 change
 \end_layout
@@ -15057,6 +15077,67 @@ If 2 masks are given instead of 1,
  print info for bonds with first atom in <mask1> and second atom in <mask2>.
 \end_layout
 
+\begin_layout Subsection
+bondparminfo
+\end_layout
+
+\begin_layout LyX-Code
+bondparminfo [parm <name> | crdset <set> | parmindex <#> | <#>] [out <file>]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+[parm
+\begin_inset space ~
+\end_inset
+
+<name>
+\begin_inset space ~
+\end_inset
+
+|
+\begin_inset space ~
+\end_inset
+
+parmindex
+\begin_inset space ~
+\end_inset
+
+<#>
+\begin_inset space ~
+\end_inset
+
+|
+\begin_inset space ~
+\end_inset
+
+<#>] Name/tag or index of topology.
+ Default is first loaded topology.
+\end_layout
+
+\begin_layout Description
+[out
+\begin_inset space ~
+\end_inset
+
+<file>] File to print to (default STDOUT).
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Print the bond parameter table with format:
+\end_layout
+
+\begin_layout LyX-Code
+#Idx Rk Req
+\end_layout
+
+\begin_layout Standard
+Where Idx is the internal bond parameter index,
+ Rk is the bond force constant (in kcal/mol*Ang^2),
+ and Req is the bond equilibrium value (in Ang.).
+\end_layout
+
 \begin_layout Subsection
 change
 \end_layout
@@ -43023,7 +43104,7 @@ vector [<name>] <Type> [out <filename> [ptrajoutput]] [<mask1>] [<mask2>]
 \end_layout
 
 \begin_layout LyX-Code
-   	[magnitude] [ired] [gridset <grid>]
+   	[magnitude] [geom] [ired] [gridset <grid>] [debye]
 \end_layout
 
 \begin_layout LyX-Code
@@ -43103,6 +43184,11 @@ ptraj
 [magnitude] Store the magnitude of the vector with aspect [Mag].
 \end_layout
 
+\begin_layout Description
+[geom] If specified,
+ use geometric centers instead of centers of mass.
+\end_layout
+
 \begin_layout Description
 [ired] Mark this vector for subsequent IRED analysis with commands 'matrix ired' and 'ired'.
 \end_layout
@@ -43129,6 +43215,14 @@ ucell[x|y|z]
 .
 \end_layout
 
+\begin_layout Description
+[debye] (
+\series bold
+'dipole'
+\series default
+ vector only) Report dipole vector in units of Debye instead of e-*Ang.
+\end_layout
+
 \begin_layout Standard
 Data Sets Created:
 \end_layout
@@ -43186,8 +43280,13 @@ dipole Store the dipole and center of mass of the atoms specified in
 <mask1>
 \series default
 .
- The vector is not converted to appropriate units,
- nor is the value well-defined if the atoms in the mask are not overall charge neutral.
+ The dipole vector has units of e-*Ang unless 
+\series bold
+'debye'
+\series default
+ is specified for units of Debye.
+ The center is always stored as simply Ang (since it is just coordinates).
+ Note that the value may not be well-defined if the atoms in the mask are not overall charge neutral.
 \end_layout
 
 \begin_layout Description

diff --git a/src/Action_Angle.cpp b/src/Action_Angle.cpp
@@ -62,6 +62,12 @@ Action::RetType Action_Angle::Setup(ActionSetup& setup) {
     mprintf("Warning: angle: One or more masks contain 0 atoms.\n");
     return Action::SKIP;
   }
+  // Check if center of mass is possible
+  if (useMass_) {
+    if (setup.Top().MaskHasZeroMass(Mask1_)) useMass_ = false;
+    if (setup.Top().MaskHasZeroMass(Mask2_)) useMass_ = false;
+    if (setup.Top().MaskHasZeroMass(Mask3_)) useMass_ = false;
+  }
   return Action::OK;  
 }
 

diff --git a/src/Action_Dihedral.cpp b/src/Action_Dihedral.cpp
@@ -91,7 +91,13 @@ Action::RetType Action_Dihedral::Setup(ActionSetup& setup) {
     mprintf("Warning: One or more masks have no atoms.\n");
     return Action::SKIP;
   }
-
+  // Check if center of mass is possible
+  if (useMass_) {
+    if (setup.Top().MaskHasZeroMass(M1_)) useMass_ = false;
+    if (setup.Top().MaskHasZeroMass(M2_)) useMass_ = false;
+    if (setup.Top().MaskHasZeroMass(M3_)) useMass_ = false;
+    if (setup.Top().MaskHasZeroMass(M4_)) useMass_ = false;
+  }
   return Action::OK;  
 }
 

diff --git a/src/Action_Distance.cpp b/src/Action_Distance.cpp
@@ -136,6 +136,13 @@ Action::RetType Action_Distance::Setup(ActionSetup& setup) {
   else
     mprintf(", imaging off");
   mprintf(".\n");
+  // Check if center of mass not possible
+  if (useMass_) {
+    if (setup.Top().MaskHasZeroMass( Mask1_ )) useMass_ = false;
+    if (mode_ == NORMAL) {
+      if (setup.Top().MaskHasZeroMass( Mask2_ )) useMass_ = false;
+    }
+  }
 
   return Action::OK;  
 }