Amber-MD
diff --git a/‎Makefile‎
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diff --git a/‎README.md‎
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diff --git a/‎configure‎
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diff --git a/‎devtools/FindMissingTests.sh‎
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diff --git a/‎devtools/GetVersionNum.sh‎
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diff --git a/‎devtools/UpdateDoxyVersion.sh‎
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diff --git a/‎devtools/converters/Extract1264.cpp‎
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diff --git a/‎doc/ChangeLog.v7.md‎
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@@ -38,7 +38,7 @@ clean: config.h
 
 docs: src/cpptraj.Doxyfile
 	cd doc && make docs
-	cd src && doxygen cpptraj.Doxyfile
+	cd src && ../devtools/UpdateDoxyVersion.sh && doxygen cpptraj.Doxyfile
 
 # Remove cpptraj binary
 uninstall: config.h
 
@@ -46,7 +46,7 @@ CPPTRAJ see the following publication:
 Disclaimer and Copyright
 ========================
 
-CPPTRAJ is Copyright (c) 2010-2025 Daniel R. Roe.
+CPPTRAJ is Copyright (c) 2010-2026 Daniel R. Roe.
 The terms for using, copying, modifying, and distributing CPPTRAJ are
 specified in the file LICENSE.
 
@@ -80,7 +80,7 @@ the following libraries:
 * Parallel NetCDF (-mpi build only, for NetCDF trajectory output in parallel)
 * CUDA (-cuda build only)
 * HIP (-hip build only)
-* FFTW (mostly optional; required for PME functionality and very large FFTs)
+* FFTW (mostly optional but recommended; required for PME functionality and very large FFTs)
 
 CPPTRAJ also makes use of the following libraries that are bundled with CPPTRAJ. External ones can be used in place of these if desired.
 
 
@@ -103,6 +103,7 @@ UsageFull() {
   echo "    -gprofile         : Use Gnu compiler GLIBC profiling (>= V4.5)*"
   echo "    -vtune            : Enable options for use with Intel Vtune."
   echo "    -single-ensemble  : Enable support for reading/writing single ensemble trajectories."
+  echo "    -leappi           : Use LEaP's value of PI for converting radians/degrees."
   echo ""
   echo "*NOTE: -profile and -gprofile are mutually exclusive."
   echo ""
@@ -202,6 +203,7 @@ icpp=0            # Used to count cmake_prefix_paths
 
 USE_SINGLEENSEMBLE=0 # Enable support for single ensemble trajectories
 USE_CPPTRAJDEBUG=0   # Enable internal cpptraj debug flags
+USE_LEAP_PI=0        # Use LEaP's value of PI for converting radians/degrees
 
 CLEAN='yes'          # yes = clean after configure, no = do not
 PERFORM_CHECKS='yes' # yes = Check compilers/libraries, no = do not
@@ -257,7 +259,7 @@ LIB_STTC[$LNETCDF]='libnetcdf.a'     # Expected static location relative to home
 LIB_D_ON[$LNETCDF]='-DBINTRAJ'       # Directive if library on
 LIB_DOFF[$LNETCDF]=''                # Directive if library off
 LIB_LINK[$LNETCDF]='dynamic'         # How to link the library
-LIB_TYPE[$LNETCDF]='ld'              # ld = LDFLAGS, cpp = cpptraj, blank = special
+LIB_TYPE[$LNETCDF]='ld'              # ld = LDFLAGS, cpp = cpptraj/libcpptraj, cpptraj=cpptraj only, blank = special
 
 LIB_STAT[$LPARANC]='off'
 LIB_CKEY[$LPARANC]='pnetcdf'
@@ -347,7 +349,7 @@ LIB_FLAG[$LSANDER]='-lsander'
 LIB_STTC[$LSANDER]=''
 LIB_D_ON[$LSANDER]='-DUSE_SANDERLIB'
 LIB_DOFF[$LSANDER]=''
-LIB_TYPE[$LSANDER]='ld'
+LIB_TYPE[$LSANDER]='cpptraj'
 
 LIB_STAT[$LTIMER]='off'
 LIB_CKEY[$LTIMER]='timer'
@@ -1334,6 +1336,7 @@ SetupFinalFlags() {
       DIRECTIVES="$DIRECTIVES -DLIBPME -DHAVE_FFTWD=1"
     fi
   fi
+  if [ $USE_LEAP_PI -eq 1 ] ; then DIRECTIVES="$DIRECTIVES -DCPPTRAJ_USE_LEAP_PI" ; fi
   # Determine if this is a GitHub or AmberTools build
   if [ ! -z "$AMBERHOME" ] ; then
     AMBCFGDIR=`pwd | grep "AmberTools/src"`
@@ -1384,6 +1387,7 @@ SetupFinalFlags() {
   # Set up include and linking flags
   ldf=''
   CPPTRAJ_LIB=''
+  CPPTRAJONLY_LIB=''
   CPPTRAJ_INC=''
   nincl=0
   for ((i=0; i < $NLIB; i++)) ; do
@@ -1420,6 +1424,8 @@ SetupFinalFlags() {
         ldf="$ldf ${LIB_FLAG[$i]}"
       elif [ "${LIB_TYPE[$i]}" = 'cpp' ] ; then
         CPPTRAJ_LIB="$CPPTRAJ_LIB ${LIB_FLAG[$i]}"
+      elif [ "${LIB_TYPE[$i]}" = 'cpptraj' ] ; then
+        CPPTRAJONLY_LIB="$CPPTRAJONLY_LIB ${LIB_FLAG[$i]}"
       fi
     fi
   done
@@ -2842,6 +2848,7 @@ while [ ! -z "$1" ] ; do
     '-nolfs'           ) LFS='' ;;
     '-single-ensemble' ) USE_SINGLEENSEMBLE=1 ;;
     '-debugon'         ) USE_CPPTRAJDEBUG=1 ;;
+    '-leappi'          ) USE_LEAP_PI=1 ;;
     # Code profiling
     '-profile'  ) USE_PROFILE=1 ;;
     '-gprofile' ) USE_PROFILE=2 ;;
@@ -2851,7 +2858,7 @@ while [ ! -z "$1" ] ; do
     '-libstatic'        ) USE_STATIC=2 ;;
     '-shared'           )
       USE_SHARED=1
-      LIB_STAT[$LSANDER]='off'
+#      LIB_STAT[$LSANDER]='off'
       ;;
     '-amberlib'         )
       if [ -z "$AMBERHOME" ] ; then
@@ -3064,12 +3071,16 @@ if [ $USE_STATIC -eq 1 ] ; then
 elif [ $USE_STATIC -eq 2 ] ; then
   echo "  Specified libraries will be linked statically if possible."
 fi
+if [ $USE_LEAP_PI -eq 1 ] ; then
+  echo "  Using LEaP's value of PI for converting radians/degrees."
+fi
 #echo DIRECTIVES $DIRECTIVES
 #echo CFLAGS $CFLAGS
 #echo CXXFLAGS $CXXFLAGS
 #echo FFLAGS $FFLAGS
 #echo LDFLAGS $LDFLAGS
 #echo CPPTRAJ_LIB $CPPTRAJ_LIB
+#echo CPPTRAJONLY_LIB $CPPTRAJONLY_LIB
 #echo CPPTRAJ_INC $CPPTRAJ_INC
 #echo REQUIRES_FLINK $REQUIRES_FLINK FLINK $FLINK
 echo ""
@@ -3179,6 +3190,7 @@ ARPACK_TARGET=$ARPACK_TARGET
 FFT_TARGET=$FFT_TARGET
 
 CPPTRAJ_LIB=$CPPTRAJ_LIB
+CPPTRAJONLY_LIB=$CPPTRAJONLY_LIB
 LDFLAGS=$LDFLAGS
 SFX=$SFX
 EXE=$EXE
 
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [ ! -f 'Makefile' ] ; then
+  echo "Should be executed in directory where main test Makefile is."
+  exit 1
+fi
+
+for DIR in `ls -d Test_*` ; do
+  if [ -d "$DIR" ] ; then
+    IN_MAKEFILE=`grep $DIR Makefile`
+    if [ -z "$IN_MAKEFILE" ] ; then
+      echo "$DIR not in Makefile."
+    fi
+  fi
+done
@@ -0,0 +1,20 @@
+#!/bin/bash
+
+EXEDIR=`dirname $0`
+
+if [ ! -d "$EXEDIR" ] ; then
+  echo "Error: Could not determine execution directory."
+  exit 1
+fi
+
+cd $EXEDIR
+
+VFILE=../src/Version.h
+if [ ! -f "$VFILE" ] ; then
+  echo "Version file $VFILE not found."
+  exit 1
+fi
+
+VERSION=`awk '{if ($2 == "CPPTRAJ_INTERNAL_VERSION") {gsub(/\"/,""); printf ("%s", $3);}}' $VFILE`
+echo $VERSION
+exit 0
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+# Update the cpptraj.Doxyfile version number
+
+EXEDIR=`dirname $0`
+
+if [ ! -d "$EXEDIR" ] ; then
+  echo "Error: Could not determine execution directory."
+  exit 1
+fi
+
+cd $EXEDIR
+DFILE=../src/cpptraj.Doxyfile
+if [ ! -f "$DFILE" ] ; then
+  echo "Doxygen file $DFILE not found."
+  exit 1
+fi
+
+VERSION=`./GetVersionNum.sh`
+if [ $? -ne 0 ] ; then
+  echo "Error: Could not get version number."
+  exit 1
+fi
+
+if [ -f 'tmp.cpptraj.Doxyfile' ] ; then
+  rm tmp.cpptraj.Doxyfile
+fi
+awk -v vstring="$VERSION" '{
+  if ($1 == "PROJECT_NUMBER")
+    printf("PROJECT_NUMBER         = %s\n", vstring);
+  else
+    print $0;
+}' $DFILE > tmp.cpptraj.Doxyfile
+mv tmp.cpptraj.Doxyfile $DFILE
+
+exit 0
@@ -0,0 +1,21 @@
+#include "ArgList.h"
+#include "BufferedLine.h"
+#include <cstdio>
+
+int main(int argc, char** argv)
+{
+  BufferedLine infile;
+  if (infile.OpenFileRead(argv[1])) return 1;
+
+  const char* ptr = infile.Line();
+  while (ptr != 0) {
+    ArgList line(ptr, "{}':, ");
+    //line.PrintDebug();
+    for (int iarg = 0; iarg < line.Nargs(); iarg += 2)
+      printf("  c4params_.insert( NameMapPair(\"%s\", %s) );\n", line[iarg].c_str(), line[iarg+1].c_str());
+    ptr = infile.Line();
+  }
+
+  infile.CloseFile();
+  return 0;
+}
@@ -0,0 +1,87 @@
+Changes in version 7.0 of CPPTRAJ. 2026
+=======================================
+
+The major change in this version is the introduction of the ability of CPPTRAJ to fully build and parameterize systems in the same way that LEaP does.
+
+New Commands
+============
+- `build` - Allow full build and parameterization of systems for MD, including CMAP, LJ 12-6-4, solvation, and ions. Includes `prepareforleap` and `fixatomorder` functionality. Can create macromolecular assemblies from PDBs with multiple models. Can solvate with a target # of solvent molecules.
+
+- `source` - Read (limited) leaprc files.
+
+- `mutate` - Mutate residues from one kind to another, keeping only common atoms.
+
+- `desc` - DEBUG: describe a selection in the same manner as leap.
+
+New functionality
+=================
+- Read topology/coordinates with the 'readdata' command.
+
+- More complete read of Amber library/prep files.
+
+- Read CMAP energy term from Amber MDOUT file.
+
+- The `permutedihedrals` command will now check rings.
+
+- The `graft` command will now use CONNECT atom information if it is present.
+
+- The `energy` command will now calculate CMAP energies (if CMAP parameters are present) and/or LJ 12-6-4 contributions to VDW energy (if `lj1264` is specified).
+
+- The `sequence` command now generates better geometries around bonds linking residues.
+
+New Keywords
+============
+- Introduce ring intersection check to `checkstructure` action.
+```
+{noringcheck | [ringshortdist <rsdist>] [ringdcut <ringdcut>]
+               [ringacut <ringacut>]}]
+```
+ Ring-bond intersections are detected when the ring center to bond center is less than <rsdist>, or less than <ringdcut> and the angle between the bond vector and ring perpendicular vector is less than <ringacut>.
+
+- Ignore extra points by default in the `checkstructure action.
+```
+[{checkxp | xpmask <xpmask>}]
+```
+If `checkxp` is specified, extra points will be included. By default, extra points will be ignored as determined by 'xpmask'; the default mask to select extra points is '&@\\XP'
+
+Add `namemap <mapset>` keywords for `change atomname from <mask>` to use an atom name map for determining new atom names.
+
+Add `gb` to `change` command to change GB radii.
+
+Add `complete` keyword to `zmatrix` command to get complete zmatrix instead of minimal zmatrix.
+
+Add `atombondorder` keyword to mol2 output; sort bonds by first atom index (similar to how leap writes mol2 files).
+
+Add `lj1264` keyword to the `energy` command to enable LJ 12-6-4 energy calculation.
+
+New file formats recognized
+===========================
+- Read Amber parameter (force field) files.
+
+- Read Amber force field modification (frcmod) files.
+
+- Read leaprc files (limited).
+
+- Read atom/pdb residue name maps.
+
+Misc Fixes
+==========
+- Fix timing percentage of solute-solvent hydrogen bonds in `hbond` action.
+
+- `replicatecell` action will correctly regenerate parameters as needed.
+
+- Fix small memory leak when calculating modes.
+
+- Ensure box information is properly updated if needed when using `crdaction`.
+
+- Improve memory allocation in the Frame class to avoid frequent reallocation of memory.
+
+- Improve handling of very large topology files.
+
+- Better handling of very small boxes with pairlist code.
+
+Not Yet Ready
+=============
+- Introduce the `byatom` keyword to `checkchirality` action to check the chirality of any atoms in specified mask that are chiral centers.
+
+- Cannot yet build topology files for polarizable force fields (IPOL > 0).