diff --git a/doc/.gitignore b/doc/.gitignore
index 8b13789179..35b5e99aee 100644
--- a/doc/.gitignore
+++ b/doc/.gitignore
@@ -1 +1 @@
-
+/html
diff --git a/doc/Developer.pdf b/doc/Developer.pdf
deleted file mode 100644
index 55b5015e49..0000000000
Binary files a/doc/Developer.pdf and /dev/null differ
diff --git a/doc/Makefile b/doc/Makefile
index 52ed2d0d73..256dcd51c6 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -1,4 +1,6 @@
 # Makefile for LAMMPS documentation
+
+SHELL 	      = /bin/bash
 SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
 BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
@@ -18,15 +20,21 @@ endif
 SOURCES=$(wildcard src/*.txt)
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean html pdf venv
+.PHONY: help clean-all clean html pdf old venv
+
+# ------------------------------------------
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
-	@echo "  html       to make HTML version of documentation using Sphinx"
-	@echo "  pdf        to make Manual.pdf"
-	@echo "  txt2html   to build txt2html tool"
-	@echo "  clean      to remove all generated RST files"
-	@echo "  clean-all  to reset the entire build environment"
+	@echo "  html       create HTML doc pages in html dir"
+	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
+	@echo "  old        create old-style HTML doc pages in old dir"
+	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
+	@echo "  clean      remove all intermediate RST files"
+	@echo "  clean-all  reset the entire build environment"
+	@echo "  txt2html   build txt2html tool"
+
+# ------------------------------------------
 
 clean-all:
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
@@ -34,8 +42,6 @@ clean-all:
 clean:
 	rm -rf $(RSTDIR)
 
-txt2html: utils/txt2html/txt2html.exe
-
 html: $(OBJECTS)
 	@(\
 		. $(VENV)/bin/activate ;\
@@ -44,20 +50,53 @@ html: $(OBJECTS)
 		deactivate ;\
 	)
 	-rm html/searchindex.js
-	-rm -rf html/_sources
+	@rm -rf html/_sources
+	@rm -rf html/PDF
+	@rm -rf html/USER
+	@cp -r src/PDF html/PDF
+	@cp -r src/USER html/USER
+	@rm -rf html/PDF/.[sg]*
+	@rm -rf html/USER/.[sg]*
+	@rm -rf html/USER/*/.[sg]*
+	@rm -rf html/USER/*/*.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
 pdf: utils/txt2html/txt2html.exe
 	@(\
 		cd src; \
 		../utils/txt2html/txt2html.exe -b *.txt; \
-		htmldoc --batch ../lammps.book;          \
+		htmldoc --batch lammps.book;          \
 		for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q $$s ../lammps.book || \
-			echo doc file $$s missing in lammps.book; done; \
+			do grep -q $$s lammps.book || \
+			echo doc file $$s missing in src/lammps.book; done; \
 		rm *.html; \
+		cd Developer; \
+		pdflatex developer; \
+		pdflatex developer; \
+		mv developer.pdf ../../Developer.pdf; \
 	)
 
+old: utils/txt2html/txt2html.exe
+	@rm -rf old
+	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
+	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
+	  mv *.html ../old; \
+	  cp Eqs/*.jpg ../old/Eqs; \
+	  cp JPG/* ../old/JPG; \
+	  cp PDF/* ../old/PDF;
+
+fetch:
+	@rm -rf html_www Manual_www.pdf Developer_www.pdf
+	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
+	@curl -s -o Developer_www.pdf http://lammps.sandia.gov/doc/Developer.pdf
+	@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
+	@tar xzf lammps-doc.tar.gz
+	@rm -f lammps-doc.tar.gz
+
+txt2html: utils/txt2html/txt2html.exe
+
+# ------------------------------------------
+
 utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
 	g++ -O -Wall -o $@ $<
 
diff --git a/doc/Manual.pdf b/doc/Manual.pdf
deleted file mode 100644
index 0f5f3497dc..0000000000
Binary files a/doc/Manual.pdf and /dev/null differ
diff --git a/doc/README b/doc/README
new file mode 100644
index 0000000000..686a1802a4
--- /dev/null
+++ b/doc/README
@@ -0,0 +1,53 @@
+Generation of LAMMPS Documentation
+
+The generation of all documentation is managed by the Makefile in this
+dir.
+
+----------------
+
+Options:
+
+make html         # generate HTML in html dir using Sphinx
+make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
+                  #   in this dir via htmldoc and pdflatex
+make old          # generate old-style HTML pages in old dir via txt2html
+make fetch        # fetch HTML doc pages and 2 PDF files from web site
+                  #   as a tarball and unpack into html dir and 2 PDFs
+make clean        # remove intermediate RST files created by HTML build
+make clean-all    # remove entire build folder and any cached data
+
+----------------
+
+Installing prerequisites for HTML build
+
+To run the HTML documention build toolchain, Python 3 and virtualenv
+have to be installed.  Here are instructions for common setups:
+
+# Ubuntu
+
+sudo apt-get install python-virtualenv
+
+# Fedora (up to version 21)
+# Red Hat Enterprise Linux or CentOS (up to version 7.x)
+
+sudo yum install python3-virtualenv
+
+# Fedora (since version 22)
+
+sudo dnf install python3-virtualenv
+
+# MacOS X
+
+## Python 3
+
+Download the latest Python 3 MacOS X package from
+https://www.python.org and install it.  This will install both Python
+3 and pip3.
+
+## virtualenv
+
+Once Python 3 is installed, open a Terminal and type
+
+pip3 install virtualenv
+
+This will install virtualenv from the Python Package Index.
diff --git a/doc/README.md b/doc/README.md
deleted file mode 100644
index b843b7eabe..0000000000
--- a/doc/README.md
+++ /dev/null
@@ -1,48 +0,0 @@
-# Generation of LAMMPS Documentation
-
-The generation of all the documentation is managed by the Makefile inside the
-`doc/` folder.
-
-## Usage:
-
-```bash
-make html         # generate HTML using Sphinx
-make pdf          # generate PDF using htmldoc
-make clean        # remove generated RST files
-make clean-all    # remove entire build folder and any cached data
-```
-
-## Installing prerequisites
-
-To run the documention build toolchain, Python 3 and virtualenv have
-to be installed. Here are instructions for common setups:
-
-### Ubuntu
-
-```bash
-sudo apt-get install python-virtualenv
-```
-
-### Fedora (up to version 21), Red Hat Enterprise Linux or CentOS (up to version 7.x)
-
-```bash
-sudo yum install python3-virtualenv
-```
-
-### Fedora (since version 22)
-
-```bash
-sudo dnf install python3-virtualenv
-```
-
-### MacOS X
-
-## Python 3
-
-Download the latest Python 3 MacOS X package from https://www.python.org and install it.
-This will install both Python 3 and pip3.
-
-## virtualenv
-
-Once Python 3 is installed, open a Terminal and type `pip3 install virtualenv`. This will
-install virtualenv from the Python Package Index.
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 3e822bd968..cd8750bd84 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="20 Sep 2016 version">
+<META NAME="docnumber" CONTENT="26 Sep 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-20 Sep 2016 version :c,h4
+26 Sep 2016 version :c,h4
 
 Version info: :h4
 
diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt
index 3e18037a83..91ec679360 100644
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@@ -501,6 +501,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "bond/create"_fix_bond_create.html,
 "bond/swap"_fix_bond_swap.html,
 "box/relax"_fix_box_relax.html,
+"cmap"_fix_cmap.html,
 "controller"_fix_controller.html,
 "deform (k)"_fix_deform.html,
 "deposit"_fix_deposit.html,
diff --git a/doc/src/Section_example.txt b/doc/src/Section_example.txt
index 90b6ff1447..d96f78fa36 100644
--- a/doc/src/Section_example.txt
+++ b/doc/src/Section_example.txt
@@ -105,8 +105,8 @@ web site.
 
 If you uncomment the "dump image"_dump_image.html line(s) in the input
 script a series of JPG images will be produced by the run (assuming
-you built LAMMPS with JPG support; see "Section start
-2.2"_Section_start.html for details).  These can be viewed
+you built LAMMPS with JPG support; see "Section
+2.2"_Section_start.html#start_2 for details).  These can be viewed
 individually or turned into a movie or animated by tools like
 ImageMagick or QuickTime or various Windows-based tools.  See the
 "dump image"_dump_image.html doc page for more details.  E.g. this
@@ -136,5 +136,5 @@ The USER directory has a large number of sub-directories which
 correspond by name to a USER package.  They contain scripts that
 illustrate how to use the command(s) provided in that package.  Many
 of the sub-directories have their own README files which give further
-instructions.  See the "Section packages"_Section_packages.html doc
+instructions.  See the "Section 4"_Section_packages.html doc
 page for more info on specific USER packages.
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index 525729a1bb..d91f7a8593 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -71,16 +71,16 @@ Package, Description, Author(s), Doc page, Example, Library
 "COMPRESS"_#COMPRESS, I/O compression, Axel Kohlmeyer (Temple U), "dump */gz"_dump.html, -, -
 "CORESHELL"_#CORESHELL, adiabatic core/shell model, Hendrik Heenen (Technical U of Munich), "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
 "DIPOLE"_#DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
-"GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
+"GPU"_#GPU, GPU-enabled styles, Mike Brown (ORNL), "Section 5.3.1"_accelerate_gpu.html, gpu, lib/gpu
 "GRANULAR"_#GRANULAR, granular systems, -, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
 "KIM"_#KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
-"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5"_accelerate_kokkos.html, kokkos, lib/kokkos
+"KOKKOS"_#KOKKOS, Kokkos-enabled styles, Trott & Moore (4), "Section 5.3.3"_accelerate_kokkos.html, kokkos, lib/kokkos
 "KSPACE"_#KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
 "MANYBODY"_#MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
 "MEAM"_#MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
 "MC"_#MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
 "MOLECULE"_#MOLECULE, molecular system force fields, -, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
-"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -
+"OPT"_#OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section 5.3.5"_accelerate_opt.html, -, -
 "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
 "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
@@ -127,7 +127,6 @@ of the LAMMPS distribution.  See the lib/package/README file for info
 on how to build the library.  If it is not listed as lib/package, then
 it is a third-party library not included in the LAMMPS distribution.
 See details on all of this below for individual packages.
-p.s.: are we ever going to get commit messages from you? ;-)
 
 :line
 
@@ -150,7 +149,7 @@ make machine :pre
 
 Make.py -p ^asphere -a machine :pre
 
-Supporting info: "Section howto 6.14"_Section_howto.html#howto_14,
+Supporting info: "Section 6.14"_Section_howto.html#howto_14,
 "pair_style gayberne"_pair_gayberne.html, "pair_style
 resquared"_pair_resquared.html,
 "doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf,
@@ -279,9 +278,8 @@ Contents: Compute and pair styles that implement the adiabatic
 core/shell model for polarizability.  The compute temp/cs command
 measures the temperature of a system with core/shell particles.  The
 pair styles augment Born, Buckingham, and Lennard-Jones styles with
-core/shell capabilities.  See "Section howto
-6.26"_Section_howto.html#howto_26 for an overview of how to use the
-package.
+core/shell capabilities.  See "Section 6.26"_Section_howto.html#howto_26
+for an overview of how to use the package.
 
 To install via make or Make.py:
 
@@ -297,8 +295,8 @@ make machine :pre
 
 Make.py -p ^coreshell -a machine :pre
 
-Supporting info: "Section howto
-6.26"_Section_howto.html#howto_26, "compute temp/cs"_compute_temp_cs.html,
+Supporting info: "Section 6.26"_Section_howto.html#howto_26,
+"compute temp/cs"_compute_temp_cs.html,
 "pair_style born/coul/long/cs"_pair_cs.html, "pair_style
 buck/coul/long/cs"_pair_cs.html, pair_style
 lj/cut/coul/long/cs"_pair_lj.html, examples/coreshell
@@ -335,7 +333,7 @@ GPU package :link(GPU),h5
 
 Contents: Dozens of pair styles and a version of the PPPM long-range
 Coulombic solver for NVIDIA GPUs.  All of them have a "gpu" in their
-style name.  "Section accelerate gpu"_accelerate_gpu.html gives
+style name.  "Section 5.3.1"_accelerate_gpu.html gives
 details of what hardware and Cuda software is required on your system,
 and how to build and use this package.  See the KOKKOS package, which
 also has GPU-enabled styles.
@@ -380,10 +378,11 @@ make machine :pre
 
 Make.py -p ^gpu -a machine :pre
 
-Supporting info: src/GPU/README, lib/gpu/README, "Section
-acclerate"_Section_accelerate.html, "Section accelerate
-gpu"_accelerate_gpu.html, Pair Styles section of "Section commands
-3.5"_Section_commands.html#cmd_5 for any pair style listed with a (g),
+Supporting info: src/GPU/README, lib/gpu/README,
+"Section 5.3"_Section_accelerate.html#acc_3,
+"Section 5.3.1"_accelerate_gpu.html,
+Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
+for any pair style listed with a (g),
 "kspace_style"_kspace_style.html, "package gpu"_package.html,
 examples/accelerate, bench/FERMI, bench/KEPLER
  
@@ -409,7 +408,7 @@ make machine :pre
 
 Make.py -p ^granular -a machine :pre
 
-Supporting info: "Section howto 6.6"_Section_howto.html#howto_6, "fix
+Supporting info: "Section 6.6"_Section_howto.html#howto_6, "fix
 pour"_fix_pour.html, "fix wall/gran"_fix_wall_gran.html, "pair_style
 gran/hooke"_pair_gran.html, "pair_style
 gran/hertz/history"_pair_gran.html, examples/pour, bench/in.chute
@@ -453,7 +452,7 @@ Contents: Dozens of atom, pair, bond, angle, dihedral, improper styles
 which run with the Kokkos library to provide optimization for
 multicore CPUs (via OpenMP), NVIDIA GPUs, or the Intel Xeon Phi (in
 native mode).  All of them have a "kk" in their style name.  "Section
-accelerate kokkos"_accelerate_kokkos.html gives details of what
+5.3.3"_accelerate_kokkos.html gives details of what
 hardware and software is required on your system, and how to build and
 use this package.  See the GPU, OPT, USER-INTEL, USER-OMP packages,
 which also provide optimizations for the same range of hardware.
@@ -473,9 +472,8 @@ the KOKKOS_ARCH setting in Makefile.kokkos_cuda), Or, as illustrated
 below, you can use the Make.py script with its "-kokkos" option to
 choose which hardware to build for.  Type "python src/Make.py -h
 -kokkos" to see the details.  If these methods do not work on your
-system, you will need to read the "Section accelerate
-kokkos"_accelerate_kokkos.html doc page for details of what
-Makefile.machine settings are needed.
+system, you will need to read the "Section 5.3.3"_accelerate_kokkos.html
+doc page for details of what Makefile.machine settings are needed.
 
 To install via make or Make.py for each of 3 hardware options:
 
@@ -495,11 +493,11 @@ make machine :pre
 
 Make.py -p ^kokkos -a machine :pre
 
-Supporting info: src/KOKKOS/README, lib/kokkos/README, "Section
-acclerate"_Section_accelerate.html, "Section accelerate
-kokkos"_accelerate_kokkos.html, Pair Styles section of "Section
-commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
-with a (k), "package kokkos"_package.html,
+Supporting info: src/KOKKOS/README, lib/kokkos/README,
+"Section 5.3"_Section_accelerate.html#acc_3,
+"Section 5.3.3"_accelerate_kokkos.html,
+Pair Styles section of "Section 3.5"_Section_commands.html#cmd_5
+for any pair style listed with a (k), "package kokkos"_package.html,
 examples/accelerate, bench/FERMI, bench/KEPLER
 
 :line
@@ -514,7 +512,7 @@ particle-mesh (PPPM), and multilevel summation method (MSM) solvers.
 Building with the KSPACE package requires a 1d FFT library be present
 on your system for use by the PPPM solvers.  This can be the KISS FFT
 library provided with LAMMPS, or 3rd party libraries like FFTW or a
-vendor-supplied FFT library.  See step 6 of "Section start
+vendor-supplied FFT library.  See step 6 of "Section
 2.2.2"_Section_start.html#start_2_2 of the manual for details of how
 to select different FFT options in your machine Makefile.  The Make.py
 tool has an "-fft" option which can insert these settings into your
@@ -536,12 +534,13 @@ make machine :pre
 Make.py -p ^kspace -a machine :pre
 
 Supporting info: "kspace_style"_kspace_style.html,
-"doc/PDF/kspace.pdf"_PDF/kspace.pdf, "Section howto
-6.7"_Section_howto.html#howto_7, "Section howto
-6.8"_Section_howto.html#howto_8, "Section howto
-6.9"_Section_howto.html#howto_9, "pair_style coul"_pair_coul.html,
-other pair style command doc pages which have "long" or "msm" in their
-style name, examples/peptide, bench/in.rhodo
+"doc/PDF/kspace.pdf"_PDF/kspace.pdf,
+"Section 6.7"_Section_howto.html#howto_7,
+"Section 6.8"_Section_howto.html#howto_8,
+"Section 6.9"_Section_howto.html#howto_9,
+"pair_style coul"_pair_coul.html, other pair style command doc pages
+which have "long" or "msm" in their style name,
+examples/peptide, bench/in.rhodo
 
 :line
  
@@ -568,7 +567,7 @@ Make.py -p ^manybody -a machine :pre
 
 Supporting info: 
  
-Examples: Pair Styles section of "Section commands
+Examples: Pair Styles section of "Section
 3.5"_Section_commands.html#cmd_5, examples/comb, examples/eim,
 examples/nb3d, examples/vashishta
 
@@ -700,9 +699,9 @@ Supporting info:"atom_style"_atom_style.html,
 "dihedral_style"_dihedral_style.html,
 "improper_style"_improper_style.html, "pair_style
 hbond/dreiding/lj"_pair_hbond_dreiding.html, "pair_style
-lj/charmm/coul/charmm"_pair_charmm.html, "Section howto
-6.3"_Section_howto.html#howto_3, examples/micelle, examples/peptide,
-bench/in.chain, bench/in.rhodo
+lj/charmm/coul/charmm"_pair_charmm.html,
+"Section 6.3"_Section_howto.html#howto_3,
+examples/micelle, examples/peptide, bench/in.chain, bench/in.rhodo
 
 :line
  
@@ -738,7 +737,7 @@ OPT package :link(OPT),h5
 Contents: A handful of pair styles with an "opt" in their style name
 which are optimized for improved CPU performance on single or multiple
 cores.  These include EAM, LJ, CHARMM, and Morse potentials.  "Section
-accelerate opt"_accelerate_opt.html gives details of how to build and
+5.3.5"_accelerate_opt.html gives details of how to build and
 use this package.  See the KOKKOS, USER-INTEL, and USER-OMP packages,
 which also have styles optimized for CPU performance.
 
@@ -763,10 +762,10 @@ make machine :pre
 
 Make.py -p ^opt -a machine :pre
 
-Supporting info: "Section acclerate"_Section_accelerate.html, "Section
-accelerate opt"_accelerate_opt.html, Pair Styles section of "Section
-commands 3.5"_Section_commands.html#cmd_5 for any pair style listed
-with an (o), examples/accelerate, bench/KEPLER
+Supporting info: "Section 5.3"_Section_accelerate.html#acc_3,
+"Section 5.3.5"_accelerate_opt.html, Pair Styles section of
+"Section 3.5"_Section_commands.html#cmd_5 for any pair style
+listed with an (t), examples/accelerate, bench/KEPLER
 
 :line
  
@@ -845,14 +844,14 @@ PYTHON package :link(PYTHON),h5
 
 Contents: A "python"_python.html command which allow you to execute
 Python code from a LAMMPS input script.  The code can be in a separate
-file or embedded in the input script itself.  See "Section python
-11.2"_Section_python.html" for an overview of using Python from
+file or embedded in the input script itself.  See "Section
+11.2"_Section_python.html#py-2 for an overview of using Python from
 LAMMPS and for other ways to use LAMMPS and Python together.
 
 Building with the PYTHON package assumes you have a Python shared
 library available on your system, which needs to be a Python 2
-version, 2.6 or later.  Python 3 is not supported.  The build uses the
-contents of the lib/python/Makefile.lammps file to find all the Python
+version, 2.6 or later.  Python 3 is not yet supported.  The build uses
+the contents of the lib/python/Makefile.lammps file to find all the Python
 files required in the build/link process.  See the lib/python/README
 file if the settings in that file do not work on your system.  Note
 that the Make.py script has a "-python" option to allow an alternate
@@ -950,7 +949,7 @@ REPLICA package :link(REPLICA),h5
 Contents: A collection of multi-replica methods that are used by
 invoking multiple instances (replicas) of LAMMPS
 simulations. Communication between individual replicas is performed in
-different ways by the different methods.  See "Section howto
+different ways by the different methods.  See "Section
 6.5"_Section_howto.html#howto_5 for an overview of how to run
 multi-replica simulations in LAMMPS.  Multi-replica methods included
 in the package are nudged elastic band (NEB), parallel replica
@@ -973,7 +972,7 @@ make machine :pre
 
 Make.py -p ^replica -a machine :pre
 
-Supporting info: "Section howto 6.5"_Section_howto.html#howto_5,
+Supporting info: "Section 6.5"_Section_howto.html#howto_5,
 "neb"_neb.html, "prd"_prd.html, "tad"_tad.html, "temper"_temper.html,
 "run_style verlet/split"_run_style.html, examples/neb, examples/prd,
 examples/tad
@@ -1148,13 +1147,13 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-EFF"_#USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
 "USER-FEP"_#USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "compute fep"_compute_fep.html, USER/fep, -, -
 "USER-H5MD"_#USER-H5MD, dump output via HDF5, Pierre de Buyl (KU Leuven), "dump h5md"_dump_h5md.html, -, -, lib/h5md
-"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
+"USER-INTEL"_#USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section 5.3.2"_accelerate_intel.html, examples/intel, -, -
 "USER-LB"_#USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
 "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, Tomas Oppelstrup & John Moriarty (LLNL), "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -, -
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
+"USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
 "USER-QTB"_#USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -, -
@@ -1353,12 +1352,12 @@ USER-DRUDE package :link(USER-DRUDE),h5
 
 Contents: This package contains methods for simulating polarizable
 systems using thermalized Drude oscillators.  It has computes, fixes,
-and pair styles for this purpose.  See "Section howto
+and pair styles for this purpose.  See "Section
 6.27"_Section_howto.html#howto_27 for an overview of how to use the
 package.  See src/USER-DRUDE/README for additional details.  There are
 auxiliary tools for using this package in tools/drude.
 
-Supporting info: "Section howto 6.27"_Section_howto.html#howto_27,
+Supporting info: "Section 6.27"_Section_howto.html#howto_27,
 src/USER-DRUDE/README, "fix drude"_fix_drude.html, "fix
 drude/transform/*"_fix_drude_transform.html, "compute
 temp/drude"_compute_temp_drude.html, "pair thole"_pair_thole.html,
@@ -1432,7 +1431,7 @@ USER-INTEL package :link(USER-INTEL),h5
 Contents: Dozens of pair, bond, angle, dihedral, and improper styles
 that are optimized for Intel CPUs and the Intel Xeon Phi (in offload
 mode).  All of them have an "intel" in their style name.  "Section
-accelerate intel"_accelerate_intel.html gives details of what hardware
+5.3.2"_accelerate_intel.html gives details of what hardware
 and compilers are required on your system, and how to build and use
 this package.  Also see src/USER-INTEL/README for more details. See
 the KOKKOS, OPT, and USER-OMP packages, which also have CPU and
@@ -1440,7 +1439,7 @@ Phi-enabled styles.
 
 Supporting info: examples/accelerate, src/USER-INTEL/TEST
 
-"Section 5"_Section_accelerate.html#acc_3
+"Section 5.3"_Section_accelerate.html#acc_3
 
 Author: Mike Brown at Intel (michael.w.brown at intel.com).  Contact
 him directly if you have questions.
@@ -1532,7 +1531,7 @@ More information about each feature can be found by reading its doc
 page in the LAMMPS doc directory.  The doc page which lists all LAMMPS
 input script commands is as follows:
 
-"Section 3"_Section_commands.html#cmd_5
+"Section 3.5"_Section_commands.html#cmd_5
 
 User-contributed features are listed at the bottom of the fix,
 compute, pair, etc sections.
@@ -1609,7 +1608,7 @@ styles, and fix styles.
  
 See this section of the manual to get started:
 
-"Section 5"_Section_accelerate.html#acc_3
+"Section 5.3"_Section_accelerate.html#acc_3
 
 The person who created this package is Axel Kohlmeyer at Temple U
 (akohlmey at gmail.com).  Contact him directly if you have questions.
diff --git a/doc/src/Section_perf.txt b/doc/src/Section_perf.txt
index fc59dbe1dc..39fe734cce 100644
--- a/doc/src/Section_perf.txt
+++ b/doc/src/Section_perf.txt
@@ -51,7 +51,7 @@ of these 5 problems on 1 or 4 cores of Linux desktop.  The bench/FERMI
 and bench/KEPLER dirs have input files and scripts and instructions
 for running the same (or similar) problems using OpenMP or GPU or Xeon
 Phi acceleration options.  See the README files in those dirs and the
-"Section accelerate"_Section_accelerate.html doc pages for
+"Section 5.3"_Section_accelerate.html#acc_3 doc pages for
 instructions on how to build LAMMPS and run on that kind of hardware.
 
 The bench/POTENTIALS directory has input files which correspond to the
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index d2202679c0..9449dbf08d 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -21,7 +21,6 @@ experienced users.
 2.8 "Screen output"_#start_8
 2.9 "Tips for users of previous versions"_#start_9 :all(b)
 
-:line
 :line
 
 2.1 What's in the LAMMPS distribution :h4,link(start_1)
@@ -70,12 +69,12 @@ launch a LAMMPS Windows executable on a Windows box.
 
 This section has the following sub-sections:
 
-"Read this first"_#start_2_1
-"Steps to build a LAMMPS executable"_#start_2_2
-"Common errors that can occur when making LAMMPS"_#start_2_3
-"Additional build tips"_#start_2_4
-"Building for a Mac"_#start_2_5
-"Building for Windows"_#start_2_6 :ul
+2.2.1 "Read this first"_#start_2_1
+2.2.1 "Steps to build a LAMMPS executable"_#start_2_2
+2.2.3 "Common errors that can occur when making LAMMPS"_#start_2_3
+2.2.4 "Additional build tips"_#start_2_4
+2.2.5 "Building for a Mac"_#start_2_5
+2.2.6 "Building for Windows"_#start_2_6 :all(b)
 
 :line
 
@@ -559,8 +558,7 @@ Typing "make clean-all" or "make clean-machine" will delete *.o object
 files created when LAMMPS is built, for either all builds or for a
 particular machine.
 
- Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
--DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
+Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
 
 As explained above, any of these 3 settings can be specified on the
 LMP_INC line in your low-level src/MAKE/Makefile.foo.
@@ -612,7 +610,7 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep.
 
 Building for a Mac :h5,link(start_2_5)
 
-OS X is BSD Unix, so it should just work.  See the
+OS X is a derivative of BSD Unix, so it should just work.  See the
 src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
 
 :line
@@ -637,9 +635,9 @@ happy to distribute contributed instructions and modifications, but
 we cannot provide support for those.
 
 With the so-called "Anniversary Update" to Windows 10, there is a
-Ubuntu subsystem available for Windows, that can be installed and
-then it can be used to compile/install LAMMPS as if you are running
-on a Ubuntu Linux system.
+Ubuntu Linux subsystem available for Windows, that can be installed
+and then used to compile/install LAMMPS as if you are running on a
+Ubuntu Linux system instead of Windows.
 
 As an alternative, you can download "daily builds" (and some older
 versions) of the installer packages from
@@ -654,10 +652,10 @@ many examples, but no source code.
 
 This section has the following sub-sections:
 
-"Package basics"_#start_3_1
-"Including/excluding packages"_#start_3_2
-"Packages that require extra libraries"_#start_3_3
-"Packages that require Makefile.machine settings"_#start_3_4 :ul
+2.3.1 "Package basics"_#start_3_1
+2.3.2 "Including/excluding packages"_#start_3_2
+2.3.3 "Packages that require extra libraries"_#start_3_3
+2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
 
 Note that the following "Section 2.4"_#start_4 describes the Make.py
 tool which can be used to install/un-install packages and build the
@@ -673,7 +671,7 @@ are always included, plus optional packages.  Packages are groups of
 files that enable a specific set of features.  For example, force
 fields for molecular systems or granular systems are in packages.
 
-"Section packages"_Section_packages.html in the manual has details
+"Section 4"_Section_packages.html in the manual has details
 about all the packages, including specific instructions for building
 LAMMPS with each package, which are covered in a more general manner
 below.
@@ -727,15 +725,15 @@ before building LAMMPS.  From the src directory, this is typically as
 simple as:
 
 make yes-colloid
-make g++ :pre
+make mpi :pre
 
 or
 
 make no-manybody
-make g++ :pre
+make mpi :pre
 
 NOTE: You should NOT include/exclude packages and build LAMMPS in a
-single make command using multiple targets, e.g. make yes-colloid g++.
+single make command using multiple targets, e.g. make yes-colloid mpi.
 This is because the make procedure creates a list of source files that
 will be out-of-date for the build if the package configuration changes
 within the same command.
@@ -826,7 +824,7 @@ where to find them.
 For libraries with provided code, the sub-directory README file
 (e.g. lib/atc/README) has instructions on how to build that library.
 This information is also summarized in "Section
-packages"_Section_packages.html.  Typically this is done by typing
+4"_Section_packages.html.  Typically this is done by typing
 something like:
 
 make -f Makefile.g++ :pre
@@ -885,17 +883,17 @@ A few packages require specific settings in Makefile.machine, to
 either build or use the package effectively.  These are the
 USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
 code performance on CPUs or other hardware, as discussed in "Section
-acclerate"_Section_accelerate.html. 
+5.3"_Section_accelerate.html#acc_3. 
 
 A summary of what Makefile.machine changes are needed for each of
-these packages is given in "Section packages"_Section_packages.html.
+these packages is given in "Section 4"_Section_packages.html.
 The details are given on the doc pages that describe each of these
 accelerator packages in detail:
 
-"USER-INTEL package"_accelerate_intel.html
-"KOKKOS package"_accelerate_kokkos.html
-"USER-OMP package"_accelerate_omp.html
-"OPT package"_accelerate_opt.html :ul
+5.3.1 "USER-INTEL package"_accelerate_intel.html
+5.3.3 "KOKKOS package"_accelerate_kokkos.html
+5.3.4 "USER-OMP package"_accelerate_omp.html
+5.3.5 "OPT package"_accelerate_opt.html :all(b)
 
 You can also look at the following machine Makefiles in
 src/MAKE/OPTIONS, which include the changes.  Note that the USER-INTEL
@@ -1367,7 +1365,7 @@ Note that the keywords do not use a leading minus sign.  I.e. the
 keyword is "t", not "-t".  Also note that each of the keywords has a
 default setting.  Example of when to use these options and what
 settings to use on different platforms is given in "Section
-5.8"_Section_accelerate.html#acc_3.
+5.3"_Section_accelerate.html#acc_3.
 
 d or device
 g or gpus
diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt
index 3527d228de..983be30f19 100644
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Section_tools.txt
@@ -107,9 +107,10 @@ The ch2lmp sub-directory contains tools for converting files
 back-and-forth between the CHARMM MD code and LAMMPS. 
 
 They are intended to make it easy to use CHARMM as a builder and as a
-post-processor for LAMMPS. Using charmm2lammps.pl, you can convert an
-ensemble built in CHARMM into its LAMMPS equivalent.  Using
-lammps2pdb.pl you can convert LAMMPS atom dumps into pdb files.
+post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
+PDB file with associated CHARMM info, including CHARMM force field
+data, into its LAMMPS equivalent.  Using lammps2pdb.pl you can convert
+LAMMPS atom dumps into PDB files.
 
 See the README file in the ch2lmp sub-directory for more information.
 
diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt
index f49c60857a..fa0607037d 100644
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@@ -156,19 +156,25 @@ CPU-only (run all-MPI or with OpenMP threading):
 
 cd lammps/src
 make yes-kokkos
-make g++ KOKKOS_DEVICES=OpenMP :pre
+make kokkos_omp :pre
 
-Intel Xeon Phi:
+CPU-only (only MPI, no threading):
 
 cd lammps/src
 make yes-kokkos
-make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC :pre
+make kokkos_mpi :pre
 
-CPUs and GPUs:
+Intel Xeon Phi (Intel Compiler, Intel MPI):
 
 cd lammps/src
 make yes-kokkos
-make cuda KOKKOS_DEVICES=Cuda :pre
+make kokkos_phi :pre
+
+CPUs and GPUs (with MPICH):
+
+cd lammps/src
+make yes-kokkos
+make kokkos_cuda_mpich :pre
 
 These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
 make command line which requires a GNU-compatible make command.  Try
@@ -180,26 +186,6 @@ first two examples above, then you *must* perform a "make clean-all"
 or "make clean-machine" before each build.  This is to force all the
 KOKKOS-dependent files to be re-compiled with the new options.
 
-You can also hardwire these make variables in the specified machine
-makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
-with a line like:
-
-KOKKOS_ARCH = KNC :pre
-
-Note that if you build LAMMPS multiple times in this manner, using
-different KOKKOS options (defined in different machine makefiles), you
-do not have to worry about doing a "clean" in between.  This is
-because the targets will be different.
-
-NOTE: The 3rd example above for a GPU, uses a different machine
-makefile, in this case src/MAKE/Makefile.cuda, which is included in
-the LAMMPS distribution.  To build the KOKKOS package for a GPU, this
-makefile must use the NVIDA "nvcc" compiler.  And it must have a
-KOKKOS_ARCH setting that is appropriate for your NVIDIA hardware and
-installed software.  Typical values for KOKKOS_ARCH are given below,
-as well as other settings that must be included in the machine
-makefile, if you create your own.
-
 NOTE: Currently, there are no precision options with the KOKKOS
 package.  All compilation and computation is performed in double
 precision.
@@ -246,7 +232,7 @@ used if running with KOKKOS_DEVICES=Pthreads for pthreads.  It is not
 necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
 provides alternative methods via environment variables for binding
 threads to hardware cores.  More info on binding threads to cores is
-given in "this section"_Section_accelerate.html#acc_3.
+given in "Section 5.3"_Section_accelerate.html#acc_3.
 
 KOKKOS_ARCH=KNC enables compiler switches needed when compling for an
 Intel Phi processor.
diff --git a/doc/src/accelerate_omp.txt b/doc/src/accelerate_omp.txt
index 74a3c82381..6e7b263c67 100644
--- a/doc/src/accelerate_omp.txt
+++ b/doc/src/accelerate_omp.txt
@@ -7,7 +7,7 @@
 
 :line
 
-"Return to Section accelerate overview"_Section_accelerate.html
+"Return to Section 5 overview"_Section_accelerate.html
 
 5.3.4 USER-OMP package :h5
 
@@ -103,8 +103,8 @@ USER-OMP style (in serial or parallel) with a single thread per MPI
 task, versus running standard LAMMPS with its standard un-accelerated
 styles (in serial or all-MPI parallelization with 1 task/core).  This
 is because many of the USER-OMP styles contain similar optimizations
-to those used in the OPT package, described in "Section accelerate
-5.3.6"_accelerate_opt.html.
+to those used in the OPT package, described in "Section
+5.3.5"_accelerate_opt.html.
 
 With multiple threads/task, the optimal choice of number of MPI
 tasks/node and OpenMP threads/task can vary a lot and should always be
diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt
index 75ff96969c..14b5e17a8d 100644
--- a/doc/src/compute_tally.txt
+++ b/doc/src/compute_tally.txt
@@ -35,7 +35,12 @@ group/group"_compute_group_group.html only that the data is
 accumulated directly during the non-bonded force computation. The
 computes {force/tally}, {pe/tally}, {stress/tally}, and
 {heat/flux/tally} are primarily provided as example how to program
-additional, more sophisticated computes using the tally mechanism.
+additional, more sophisticated computes using the tally callback
+mechanism. Compute {pe/mol/tally} is one such style, that can
+- through using this mechanism - separately tally intermolecular
+and intramolecular energies. Something that would otherwise be
+impossible without integrating this as a core functionality into
+the based classes of LAMMPS.
 
 :line
 
@@ -56,7 +61,7 @@ atom scalar (the contributions of the single atom to the global
 scalar). Compute {pe/mol/tally} calculates a global 4-element vector
 containing (in this order): {evdwl} and {ecoul} for intramolecular pairs
 and {evdwl} and {ecoul} for intermolecular pairs. Since molecules are
-identified my their molecule IDs, the partitioning does not have to be
+identified by their molecule IDs, the partitioning does not have to be
 related to molecules, but the energies are tallied into the respective
 slots depending on whether the molecule IDs of a pair are the same or
 different. Compute {force/tally} calculates a global scalar (the force
diff --git a/doc/src/dump.txt b/doc/src/dump.txt
index 694295699b..8173de82d7 100644
--- a/doc/src/dump.txt
+++ b/doc/src/dump.txt
@@ -328,8 +328,8 @@ bonds and colors.
 
 Note that {atom}, {custom}, {dcd}, {xtc}, and {xyz} style dump files
 can be read directly by "VMD"_http://www.ks.uiuc.edu/Research/vmd, a
-popular molecular viewing program.  See "Section
-tools"_Section_tools.html#vmd of the manual and the
+popular molecular viewing program.  See
+"Section 9"_Section_tools.html#vmd of the manual and the
 tools/lmp2vmd/README.txt file for more information about support in
 VMD for reading and visualizing LAMMPS dump files.
 
@@ -390,7 +390,7 @@ Using MPI-IO requires two steps.  First, build LAMMPS with its MPIIO
 package installed, e.g.
 
 make yes-mpiio    # installs the MPIIO package
-make g++          # build LAMMPS for your platform :pre
+make mpi          # build LAMMPS for your platform :pre
 
 Second, use a dump filename which contains ".mpiio".  Note that it
 does not have to end in ".mpiio", just contain those characters.
@@ -531,7 +531,7 @@ so that each value is 0.0 to 1.0.  If the simulation box is triclinic
 (tilted), then all atom coords will still be between 0.0 and 1.0.
 I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
 the non-orthogonal vectors of the simulation box edges, as discussed
-in "Section howto 6.12"_Section_howto.html#howto_12.
+in "Section 6.12"_Section_howto.html#howto_12.
 
 Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
 image flags for each atom.  Unwrapped means that if the atom has
diff --git a/doc/src/dump_molfile.txt b/doc/src/dump_molfile.txt
index 5dd045ec2d..3494ba9a91 100644
--- a/doc/src/dump_molfile.txt
+++ b/doc/src/dump_molfile.txt
@@ -34,7 +34,7 @@ to one or more files every N timesteps in one of several formats.
 Only information for atoms in the specified group is dumped.  This
 specific dump style uses molfile plugins that are bundled with the
 "VMD"_http://www.ks.uiuc.edu/Research/vmd molecular visualization and
-analysis program.  See "Section tools"_Section_tools.html#vmd of the
+analysis program.  See "Section 9"_Section_tools.html#vmd of the
 manual and the tools/lmp2vmd/README.txt file for more information
 about support in VMD for reading and visualizing native LAMMPS dump
 files.
diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt
new file mode 100644
index 0000000000..924e6f5022
--- /dev/null
+++ b/doc/src/fix_cmap.txt
@@ -0,0 +1,132 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix cmap command :h3
+
+[Syntax:]
+
+fix ID group-ID cmap filename :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+cmap = style name of this fix command
+filename = force-field file with CMAP coefficients :ul
+
+[Examples:]
+
+fix            myCMAP all cmap ../potentials/cmap36.data
+read_data      proteinX.data fix myCMAP crossterm CMAP
+fix_modify     myCMAP energy yes :pre
+
+[Description:]
+
+This command enables CMAP crossterms to be added to simulations which
+use the CHARMM force field.  These are relevant for any CHARMM model
+of a peptide or protein sequences that is 3 or more amino-acid
+residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks for details,
+including the analytic energy expressions for CMAP interactions.  The
+CMAP crossterms add additional potential energy contributions to pairs
+of overlapping phi-psi dihedrals of amino-acids, which are important
+to properly represent their conformational behavior.
+
+The examples/cmap directory has a sample input script and data file
+for a small peptide, that illustrates use of the fix cmap command.
+
+As in the example above, this fix should be used before reading a data
+file that contains a listing of CMAP interactions.  The {filename}
+specified should contain the CMAP parameters for a particular version
+of the CHARMM force field.  Two such files are including in the
+lammps/potentials directory: charmm22.cmap and charmm36.cmap.
+
+The data file read by the "read_data" must contain the topology of all
+the CMAP interactions, similar to the topology data for bonds, angles,
+dihedrals, etc.  Specically it should have a line like this
+in its header section:
+
+N crossterms :pre
+
+where N is the number of CMAP crossterms.  It should also have a section
+in the body of the data file like this with N lines:
+
+CMAP :pre
+
+       1       1       8      10      12      18      20
+       2       5      18      20      22      25      27
+       ... 
+       N       3     314     315     317      318    330 :pre
+
+The first column is an index from 1 to N to enumerate the CMAP terms;
+it is ignored by LAMMPS.  The 2nd column is the "type" of the
+interaction; it is an index into the CMAP force field file.  The
+remaining 5 columns are the atom IDs of the atoms in the two 4-atom
+dihedrals that overlap to create the CMAP 5-body interaction.  Note
+that the "crossterm" and "CMAP" keywords for the header and body
+sections match those specified in the read_data command following the
+data file name; see the "read_data"_doc/read_data.html doc page for
+more details.
+
+A data file containing CMAP crossterms can be generated from a PDB
+file using the charmm2lammps.pl script in the tools/ch2lmp directory
+of the LAMMPS distribution.  The script must be invoked with the
+optional "-cmap" flag to do this; see the tools/ch2lmp/README file for
+more information.
+
+The potential energy associated with CMAP interactions can be output
+as described below.  It can also be included in the total potential
+energy of the system, as output by the
+"thermo_style"_thermo_style.html command, if the "fix_modify
+energy"_fix_modify.html command is used, as in the example above.  See
+the note below about how to include the CMAP energy when performing an
+"energy minimization"_minimize.html.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the potential "energy" of the CMAP interactions system's
+potential energy as part of "thermodynamic output"_thermo_style.html.
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Section_howto.html#howto_15.  The scalar is the
+potential energy discussed above.  The scalar value calculated by this
+fix is "extensive".
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.
+
+The forces due to this fix are imposed during an energy minimization,
+invoked by the "minimize"_minimize.html command.
+
+NOTE: If you want the potential energy associated with the CMAP terms
+forces to be included in the total potential energy of the system (the
+quantity being minimized), you MUST enable the
+"fix_modify"_fix_modify.html {energy} option for this fix.
+
+[Restrictions:]
+
+This fix can only be used if LAMMPS was built with the MOLECULE
+package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.
+
+[Related commands:]
+
+"fix_modify"_fix_modify.html, "read_data"_read_data.html
+
+[Default:] none
+
+:line
+
+(Buck) 
+Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36
+(2006).
+
+(Brooks) 
+Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt
index 46f8f57c33..b228a7c851 100644
--- a/doc/src/fix_phonon.txt
+++ b/doc/src/fix_phonon.txt
@@ -43,10 +43,11 @@ fix 1 all phonon 10 5000 500000 GAMMA EAM0D nasr 100 :pre
 Calculate the dynamical matrix from molecular dynamics simulations
 based on fluctuation-dissipation theory for a group of atoms.
 
-Consider a crystal with \(N\) unit cells in three dimensions labelled \(l = (l_1, l_2, l_3)\) where \(l_i\)
-are integers.  Each unit cell is defined by three linearly independent
-vectors \(\mathbf\{a\}_1\), \(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a
-parallelipiped, containing \(K\) basis atoms labeled \(k\).
+Consider a crystal with \(N\) unit cells in three dimensions labelled
+\(l = (l_1, l_2, l_3)\) where \(l_i\) are integers.  Each unit cell is
+defined by three linearly independent vectors \(\mathbf\{a\}_1\),
+\(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelipiped,
+containing \(K\) basis atoms labeled \(k\).
 
 Based on fluctuation-dissipation theory, the force constant
 coefficients of the system in reciprocal space are given by
@@ -62,18 +63,16 @@ where \(\mathbf\{G\}\) is the Green's functions coefficients given by
 \mathbf\{G\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) = \left< \mathbf\{u\}_\{k\alpha\}(\mathbf\{q\}) \bullet \mathbf\{u\}_\{k^\prime \beta\}^*(\mathbf\{q\}) \right>
 \end\{equation\}
 
-
 where \(\left< \ldots \right>\) denotes the ensemble average, and
 
 \begin\{equation\}
 \mathbf\{u\}_\{k\alpha\}(\mathbf\{q\}) = \sum_l \mathbf\{u\}_\{l k \alpha\} \exp\{(i\mathbf\{qr\}_l)\}
 \end\{equation\}
 
-
-is the \(\alpha\) component of the atomic displacement for the \(k\) th atom
-in the unit cell in reciprocal space at \(\mathbf\{q\}\). In practice, the Green's
-functions coefficients can also be measured according to the following
-formula,
+is the \(\alpha\) component of the atomic displacement for the \(k\)
+th atom in the unit cell in reciprocal space at \(\mathbf\{q\}\). In
+practice, the Green's functions coefficients can also be measured
+according to the following formula,
 
 \begin\{equation\}
 \mathbf\{G\}_\{k\alpha,k^\prime \beta\}(\mathbf\{q\}) =
@@ -81,12 +80,13 @@ formula,
 - \left<\mathbf\{R\}\right>_\{k \alpha\}(\mathbf\{q\}) \bullet \left<\mathbf\{R\}\right>^*_\{k^\prime \beta\}(\mathbf\{q\})
 \end\{equation\}
 
-where \(\mathbf\{R\}\) is the instantaneous positions of atoms, and \(\left<\mathbf\{R\}\right>\) is the
-averaged atomic positions. It gives essentially the same results as
-the displacement method and is easier to implement in an MD code.
+where \(\mathbf\{R\}\) is the instantaneous positions of atoms, and
+\(\left<\mathbf\{R\}\right>\) is the averaged atomic positions. It
+gives essentially the same results as the displacement method and is
+easier to implement in an MD code.
 
-Once the force constant matrix is known, the dynamical matrix \(\mathbf\{D\}\) can
-then be obtained by
+Once the force constant matrix is known, the dynamical matrix
+\(\mathbf\{D\}\) can then be obtained by
 
 \begin\{equation\}
 \mathbf\{D\}_\{k\alpha, k^\prime\beta\}(\mathbf\{q\}) =
@@ -100,10 +100,11 @@ two-point correlations.  To achieve this. the positions of the atoms
 are examined every {Nevery} steps and are Fourier-transformed into
 reciprocal space, where the averaging process and correlation
 computation is then done.  After every {Noutput} measurements, the
-matrix \(\mathbf\{G\}(\mathbf\{q\})\) is calculated and inverted to obtain the elastic
-stiffness coefficients.  The dynamical matrices are then constructed
-and written to {prefix}.bin.timestep files in binary format and to the
-file {prefix}.log for each wavevector \(\mathbf\{q\}\).
+matrix \(\mathbf\{G\}(\mathbf\{q\})\) is calculated and inverted to
+obtain the elastic stiffness coefficients.  The dynamical matrices are
+then constructed and written to {prefix}.bin.timestep files in binary
+format and to the file {prefix}.log for each wavevector
+\(\mathbf\{q\}\).
 
 A detailed description of this method can be found in
 ("Kong2011"_#Kong2011).
@@ -126,12 +127,13 @@ which lattice point; the lattice indices start from 0. An auxiliary
 code, "latgen"_http://code.google.com/p/latgen, can be employed to
 generate the compatible map file for various crystals.
 
-In case one simulates an aperiodic system, where the whole simulation box
-is treated as a unit cell, one can set {map_file} as {GAMMA}, so that the mapping
-info will be generated internally and a file is not needed. In this case, the
-dynamical matrix at only the gamma-point will/can be evaluated. Please keep in
-mind that fix-phonon is designed for cyrstals, it will be inefficient and
-even degrade the performance of lammps in case the unit cell is too large.
+In case one simulates an aperiodic system, where the whole simulation
+box is treated as a unit cell, one can set {map_file} as {GAMMA}, so
+that the mapping info will be generated internally and a file is not
+needed. In this case, the dynamical matrix at only the gamma-point
+will/can be evaluated. Please keep in mind that fix-phonon is designed
+for cyrstals, it will be inefficient and even degrade the performance
+of lammps in case the unit cell is too large.
 
 The calculated dynamical matrix elements are written out in
 "energy/distance^2/mass"_units.html units.  The coordinates for {q}
diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt
index 23128042c0..54df431d2b 100755
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
@@ -99,8 +99,8 @@ center-of-mass fixed during the thermodynamic integration. A nonzero
 total velocity will result in divergences during the integration due
 to the fact that the atoms are 'attached' to their equilibrium
 positions by the Einstein crystal. Check the option {zero} of "fix
-langevin"_fix_langevin_html and "velocity"_velocity.html. The use of
-the Nose-Hoover thermostat ("fix nvt"_fix_nvt.html) is {NOT}
+langevin"_fix_langevin.html and "velocity"_velocity.html. The use of
+the Nose-Hoover thermostat ("fix nvt"_fix_nh.html) is {NOT}
 recommended due to its well documented issues with the canonical
 sampling of harmonic degrees of freedom (notice that the {chain}
 option will {NOT} solve this problem). The Langevin thermostat ("fix
diff --git a/doc/src/fix_wall_region.txt b/doc/src/fix_wall_region.txt
index 198540e7da..8c38e6316f 100644
--- a/doc/src/fix_wall_region.txt
+++ b/doc/src/fix_wall_region.txt
@@ -85,8 +85,10 @@ to feel no force (they don't "see" the wall) when in one location,
 then move a distance epsilon, and suddenly feel a large force because
 they now "see" the wall.  In a worst-case scenario, this can blow
 particles out of the simulation box.  Thus, as a general rule you
-should not use the fix wall/region command with {union} or
-{interesect} regions that have convex points or edges.
+should not use the fix wall/gran/region command with {union} or
+{interesect} regions that have convex points or edges resulting from
+the union/intersection (convex points/edges in the union/intersection
+due to a single sub-region are still OK).
 
 NOTE: Similarly, you should not define {union} or {intersert} regions
 for use with this command that share an overlapping common face that
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index f1a481fc3b..fc4a749cc6 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -138,7 +138,6 @@ Fixes :h1
    fix_temp_rescale_eff
    fix_tfmc
    fix_thermal_conductivity
-   fix_ti_rs
    fix_ti_spring
    fix_tmd
    fix_ttm
diff --git a/doc/lammps.book b/doc/src/lammps.book
similarity index 99%
rename from doc/lammps.book
rename to doc/src/lammps.book
index f28bb48b56..620eee483d 100644
--- a/doc/lammps.book
+++ b/doc/src/lammps.book
@@ -247,7 +247,6 @@ fix_smd_integrate_tlsph.html
 fix_smd_integrate_ulsph.html
 fix_smd_move_triangulated_surface.html
 fix_smd_setvel.html
-fix_smd_tlsph_reference_configuration.html
 fix_smd_wall_surface.html
 fix_spring.html
 fix_spring_chunk.html
@@ -262,7 +261,6 @@ fix_temp_rescale.html
 fix_temp_rescale_eff.html
 fix_tfmc.html
 fix_thermal_conductivity.html
-fix_ti_rs.html
 fix_ti_spring.html
 fix_tmd.html
 fix_ttm.html
diff --git a/doc/src/package.txt b/doc/src/package.txt
index 7faf952121..4556fb2d29 100644
--- a/doc/src/package.txt
+++ b/doc/src/package.txt
@@ -142,7 +142,7 @@ the style options are set, either to default values or to specified
 settings.  I.e. settings from previous invocations do not persist
 across multiple invocations.
 
-See the "Section Accelerate"_Section_accelerate.html section of the
+See the "Section 5.3"_Section_accelerate.html#acc_3 section of the
 manual for more details about using the various accelerator packages
 for speeding up LAMMPS simulations.
 
diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt
index 40f449e98b..7cb2d0aeae 100644
--- a/doc/src/pair_gauss.txt
+++ b/doc/src/pair_gauss.txt
@@ -63,7 +63,7 @@ solvent simulations of salt ions "(Lenart)"_#Lenart and of surfactants
 "(Jusufi)"_#Jusufi.  In these instances the Gaussian potential mimics
 the hydration barrier between a pair of particles. The hydration
 barrier is located at r_mh and has a width of sigma_h. The prefactor
-determines the hight of the potential barrier.
+determines the height of the potential barrier.
 
 The following coefficients must be defined for each pair of atom types
 via the "pair_coeff"_pair_coeff.html command as in the example above,
@@ -73,9 +73,11 @@ commands:
 
 H (energy * distance units)
 r_mh (distance units)
-sigma_h (distance units) :ul
+sigma_h (distance units)
+cutoff (distance units) :ul
 
-The global cutoff (r_c) specified in the pair_style command is used.
+The last coefficient is optional. If not specified, the global cutoff
+is used.
 
 :line
 
diff --git a/doc/src/python.txt b/doc/src/python.txt
index 2ec2fdcfca..aa6b0cd09c 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -97,7 +97,7 @@ be passed to various commands as arguments, so that the variable is
 evaluated during a simulation run.
 
 A broader overview of how Python can be used with LAMMPS is
-given in "Section python"_Section_python.html.  There is an
+given in "Section 11"_Section_python.html.  There is an
 examples/python directory which illustrates use of the python
 command.
 
diff --git a/doc/src/read_restart.txt b/doc/src/read_restart.txt
index 0e50b4028c..1f15169774 100644
--- a/doc/src/read_restart.txt
+++ b/doc/src/read_restart.txt
@@ -124,7 +124,7 @@ MPI-IO requires two steps.  First, build LAMMPS with its MPIIO package
 installed, e.g.
 
 make yes-mpiio    # installs the MPIIO package
-make g++          # build LAMMPS for your platform :pre
+make mpi          # build LAMMPS for your platform :pre
 
 Second, use a restart filename which contains ".mpiio".  Note that it
 does not have to end in ".mpiio", just contain those characters.
diff --git a/doc/src/region.txt b/doc/src/region.txt
index 99417122ba..71dd8ee262 100644
--- a/doc/src/region.txt
+++ b/doc/src/region.txt
@@ -186,7 +186,7 @@ functions, and include "thermo_style"_thermo_style.html command
 keywords for the simulation box parameters and timestep and elapsed
 time.  Thus it is easy to specify a time-dependent radius.
 
-See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages
+See "Section 6.12"_Section_howto.html#howto_12 of the doc pages
 for a geometric description of triclinic boxes, as defined by LAMMPS,
 and how to transform these parameters to and from other commonly used
 triclinic representations.
@@ -361,7 +361,7 @@ sub-regions can be defined with the {open} keyword.
 Styles with a {kk} suffix are functionally the same as the
 corresponding style without the suffix.  They have been optimized to
 run faster, depending on your available hardware, as discussed in
-"Section_accelerate"_Section_accelerate.html of the manual.  The
+"Section 5"_Section_accelerate.html of the manual.  The
 accelerated styles take the same arguments and should produce the same
 results, except for round-off and precision issues.
 
@@ -378,7 +378,7 @@ by including their suffix, or you can use the "-suffix command-line
 switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
 use the "suffix"_suffix.html command in your input script.
 
-See "Section_accelerate"_Section_accelerate.html of the manual for
+See "Section 5"_Section_accelerate.html of the manual for
 more instructions on how to use the accelerated styles effectively.
 
 :line
diff --git a/doc/src/restart.txt b/doc/src/restart.txt
index 48a1ac7d42..855ee043e0 100644
--- a/doc/src/restart.txt
+++ b/doc/src/restart.txt
@@ -82,7 +82,7 @@ versions 2.0 and above.  Using MPI-IO requires two steps.  First,
 build LAMMPS with its MPIIO package installed, e.g.
 
 make yes-mpiio    # installs the MPIIO package
-make g++          # build LAMMPS for your platform :pre
+make mpi          # build LAMMPS for your platform :pre
 
 Second, use a restart filename which contains ".mpiio".  Note that it
 does not have to end in ".mpiio", just contain those characters.
diff --git a/doc/src/variable.txt b/doc/src/variable.txt
index 7940f2b5e9..2f048ba810 100644
--- a/doc/src/variable.txt
+++ b/doc/src/variable.txt
@@ -1121,7 +1121,7 @@ with a leading $ sign (e.g. $x or $\{abc\}) versus with a leading "v_"
 (e.g. v_x or v_abc).  The former can be used in any input script
 command, including a variable command.  The input script parser
 evaluates the reference variable immediately and substitutes its value
-into the command.  As explained in "Section commands
+into the command.  As explained in "Section
 3.2"_Section_commands.html#cmd_2 for "Parsing rules", you can also use
 un-named "immediate" variables for this purpose.  For example, a
 string like this $((xlo+xhi)/2+sqrt(v_area)) in an input script
diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt
index d162c35334..27b83a015b 100644
--- a/doc/src/velocity.txt
+++ b/doc/src/velocity.txt
@@ -139,7 +139,7 @@ if rot = yes, the angular momentum is zeroed.
 If specified, the {temp} keyword is used by {create} and {scale} to
 specify a "compute"_compute.html that calculates temperature in a
 desired way, e.g. by first subtracting out a velocity bias, as
-discussed in "Section howto 16"_Section_howto.html#howto_15 of the doc
+discussed in "Section 6.16"_Section_howto.html#howto_16 of the doc
 pages.  If this keyword is not specified, {create} and {scale}
 calculate temperature using a compute that is defined internally as
 follows:
@@ -161,8 +161,8 @@ The {bias} keyword with a {yes} setting is used by {create} and
 If the temperature compute also calculates a velocity bias, the the
 bias is subtracted from atom velocities before the {create} and
 {scale} operations are performed.  After the operations, the bias is
-added back to the atom velocities.  See "Section howto
-16"_Section_howto.html#howto_15 of the doc pages for more discussion
+added back to the atom velocities.  See "Section
+6.16"_Section_howto.html#howto_16 of the doc pages for more discussion
 of temperature computes with biases.  Note that the velocity bias is
 only applied to atoms in the temperature compute specified with the
 {temp} keyword.
diff --git a/doc/src/write_restart.txt b/doc/src/write_restart.txt
index b324ea320e..8160eec3df 100644
--- a/doc/src/write_restart.txt
+++ b/doc/src/write_restart.txt
@@ -55,7 +55,7 @@ versions 2.0 and above.  Using MPI-IO requires two steps.  First,
 build LAMMPS with its MPIIO package installed, e.g.
 
 make yes-mpiio    # installs the MPIIO package
-make g++          # build LAMMPS for your platform :pre
+make mpi          # build LAMMPS for your platform :pre
 
 Second, use a restart filename which contains ".mpiio".  Note that it
 does not have to end in ".mpiio", just contain those characters.
diff --git a/examples/README b/examples/README
index 400d69aa2d..462fa93e12 100644
--- a/examples/README
+++ b/examples/README
@@ -61,6 +61,7 @@ sub-directories:
 accelerate: use of all the various accelerator packages
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
+cmap:     CMAP 5-body contributions to CHARMM force field
 colloid:  big colloid particles in a small particle solvent, 2d system
 coreshell: adiabatic core/shell model
 comb:	  models using the COMB potential
diff --git a/examples/USER/misc/ti/in.ti_spring b/examples/USER/misc/ti/in.ti_spring
old mode 100755
new mode 100644
diff --git a/examples/cmap/charmm22.cmap b/examples/cmap/charmm22.cmap
new file mode 100644
index 0000000000..782dcc5dbf
--- /dev/null
+++ b/examples/cmap/charmm22.cmap
@@ -0,0 +1,1022 @@
+# Title: charmm correction map
+
+#  alanine map, type 1
+
+# -180
+0.126790 0.768700 0.971260 1.250970 2.121010
+2.695430 2.064440 1.764790 0.755870 -0.713470
+0.976130 -2.475520 -5.455650 -5.096450 -5.305850
+-3.975630 -3.088580 -2.784200 -2.677120 -2.646060
+-2.335350 -2.010440 -1.608040 -0.482250
+
+# -165
+-0.802290 1.377090 1.577020 1.872290 2.398990
+2.461630 2.333840 1.904070 1.061460 0.518400
+-0.116320 -3.575440 -5.284480 -5.160310 -4.196010
+-3.276210 -2.715340 -1.806200 -1.101780 -1.210320
+-1.008810 -0.637100 -1.603360 -1.776870
+
+# -150
+-0.634810 1.156210 1.624350 2.047200 2.653910
+2.691410 2.296420 1.960450 1.324930 2.038290
+-1.151510 -3.148610 -4.058280 -4.531850 -3.796370
+-2.572090 -1.727250 -0.961410 -0.282910 -0.479120
+-1.039340 -1.618060 -1.725460 -1.376360
+
+# -135
+0.214000 1.521370 1.977440 2.377950 2.929470
+2.893410 2.435810 2.162970 1.761500 1.190090
+-1.218610 -2.108900 -2.976100 -3.405340 -2.768440
+-1.836030 -0.957950 0.021790 -0.032760 -0.665880
+-1.321170 -1.212320 -0.893170 -0.897040
+
+# -120
+0.873950 1.959160 2.508990 2.841100 3.698960
+3.309330 2.614300 2.481720 2.694660 1.082440
+-0.398320 -1.761800 -2.945110 -3.294690 -2.308300
+-0.855480 -0.087320 0.439040 0.691880 -0.586330
+-1.027210 -0.976640 -0.467580 0.104020
+
+# -105
+1.767380 2.286650 2.818030 3.065500 3.370620
+3.397440 2.730310 2.878790 2.542010 1.545240
+-0.092150 -1.694440 -2.812310 -2.802430 -1.856360
+-0.306240 -0.122440 0.444680 0.810150 -0.058630
+-0.270290 -0.178830 0.202360 0.493810
+
+# -90
+1.456010 2.743180 2.589450 3.046230 3.451510
+3.319160 3.052900 3.873720 2.420650 0.949100
+0.008370 -1.382980 -2.138930 -2.087380 -1.268300
+-0.494370 0.267580 0.908250 0.537520 0.306260
+0.069540 0.097460 0.263060 0.603220
+
+# -75
+1.396790 3.349090 2.180920 2.942960 3.814070
+3.675800 3.555310 3.887290 2.101260 -0.190940
+-0.732240 -1.382040 -0.673880 -0.817390 -0.826980
+-0.111800 0.053710 0.296400 0.692240 0.428960
+-0.036100 -0.033820 -0.194300 0.400210
+
+# -60
+0.246650 1.229980 1.716960 3.168570 4.208190
+4.366860 4.251080 3.348110 0.997540 -1.287540
+-1.179900 -0.684300 -0.853660 -1.158760 -0.347550
+0.114810 0.242800 0.322420 0.370140 -0.374950
+-0.676940 -1.323430 -1.366650 -0.218770
+
+# -45
+-1.196730 0.078060 2.347410 4.211350 5.376000
+5.364940 4.355200 2.436510 0.408470 -0.590840
+-0.435960 -0.501210 -0.822230 -0.607210 0.057910
+0.246580 -0.070570 0.379430 0.247770 -0.571680
+-1.282910 -1.715770 -1.839820 -1.987110
+
+# -30
+-1.174720 1.067030 4.180460 6.741610 6.070770
+4.781470 2.758340 1.295810 0.571150 -0.196480
+0.251860 -0.732140 1.289360 1.497590 1.890550
+2.198490 0.169290 0.534000 0.331780 -1.276320
+-2.550070 -3.312150 -3.136670 -2.642260
+
+# -15
+0.293590 5.588070 3.732620 3.217620 3.272450
+2.492320 1.563700 1.356760 0.831410 0.630170
+1.591970 0.821920 0.486070 0.715760 0.996020
+1.591580 -0.367400 0.181770 -0.613920 -2.267900
+-3.516460 -3.597700 -3.043340 -1.765020
+
+# 0
+2.832310 0.787990 0.323280 0.479230 0.628600
+0.976330 1.238750 1.671950 1.645480 2.520340
+1.606970 0.776350 0.119780 0.070390 0.121170
+-1.569230 -1.213010 -1.846360 -2.744510 -3.792530
+-3.934880 -3.615930 -2.675750 -0.924170
+
+# 15
+-0.778340 -1.912680 -2.052140 -1.846280 -1.047430
+0.183400 1.682950 2.223500 1.358370 2.448660
+1.436920 0.678570 -0.237060 -0.535320 -0.790380
+-2.182580 -3.251140 -4.195110 -4.269270 -3.908210
+-3.455620 -2.773970 1.755370 0.313410
+
+# 30
+-2.963810 -3.483730 -3.517080 -2.724860 -1.405510
+0.336200 1.428450 1.394630 0.970370 2.462720
+1.522430 0.553620 -0.407380 -1.482950 -3.613920
+-4.159810 -4.945580 -4.784040 -3.764540 -2.959140
+-1.963850 -1.071260 -1.599580 -2.445320
+
+# 45
+-4.029070 -3.932660 -3.558480 -2.513980 -1.037320
+0.362000 0.814380 0.754110 0.502370 1.903420
+0.770220 -0.416420 -3.286310 -3.875270 -4.907800
+-5.704430 -5.645660 -4.396040 -2.865450 -2.368170
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+# 60
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+-3.756430 -3.640810 -3.640430 -3.550690
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+# 75
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+-4.161970 -3.725150 -3.715310 -2.606760
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+# 90
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+-2.793220 -3.828560 -5.211800 -6.636850 -6.989940
+-6.108800 -5.452410 -3.911450 -4.321000 -4.587240
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+# 105
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+-3.014400 -4.481110 -6.053510 -6.865400 -6.871130
+-5.728240 -3.912230 -4.802110 -5.034640 -4.715990
+-4.601080 -4.086220 -3.274630 -2.410940
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+# 120
+-1.969230 -1.116650 -0.540250 -0.150330 0.763520
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+-3.366270 -5.008260 -6.124810 -7.034830 -6.724320
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+-4.444320 -4.004260 -3.415720 -2.751230
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+# 135
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+-3.469470 -4.946030 -6.112560 -1.915580 -4.047310
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+-4.494620 -4.442210 -4.163570 -3.183510
+
+# 150
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+-5.390070 -4.783930 -4.190630 -4.115420 -4.042280
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+# 165
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+-2.736530 -0.735240 -4.563830 -6.408350 -5.889450
+-5.141750 -4.194970 -3.666490 -3.843450 -3.818830
+-3.826180 -3.596820 -2.994790 -2.231020
+
+#  alanine before proline map, type 2
+
+# -180
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+# -165
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+# -150
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+-2.572090 -1.727250 -0.961410 -0.282910 -0.479120
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+
+# -135
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+-1.218610 -2.108900 -2.976100 -3.405340 -2.768440
+-1.836030 -0.957950 0.021790 -0.032760 -0.665880
+-1.321170 -1.212320 -0.893170 -0.897040
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+# -120
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+-0.398320 -1.761800 -2.945110 -3.294690 -2.308300
+-0.855480 -0.087320 0.439040 0.691880 -0.586330
+-1.027210 -0.976640 -0.467580 0.104020
+
+# -105
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+-0.306240 -0.122440 0.444680 0.810150 -0.058630
+-0.270290 -0.178830 0.202360 0.493810
+
+# -90
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+-0.494370 0.267580 0.908250 0.537520 0.306260
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+
+# -75
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+-0.732240 -1.382040 -0.673880 -0.817390 -0.826980
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+-0.036100 -0.033820 -0.194300 0.400210
+
+# -60
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+-1.179900 -0.684300 -0.853660 -1.158760 -0.347550
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+-0.676940 -1.323430 -1.366650 -0.218770
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+# -45
+-1.196730 0.078060 2.347410 4.211350 5.376000
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+-0.435960 -0.501210 -0.822230 -0.607210 0.057910
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+-1.282910 -1.715770 -1.839820 -1.987110
+
+# -30
+-1.174720 1.067030 4.180460 6.741610 6.070770
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+-2.550070 -3.312150 -3.136670 -2.642260
+
+# -15
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+-3.516460 -3.597700 -3.043340 -1.765020
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+# 0
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+-1.569230 -1.213010 -1.846360 -2.744510 -3.792530
+-3.934880 -3.615930 -2.675750 -0.924170
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+# 15
+-0.778340 -1.912680 -2.052140 -1.846280 -1.047430
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+-2.182580 -3.251140 -4.195110 -4.269270 -3.908210
+-3.455620 -2.773970 1.755370 0.313410
+
+# 30
+-2.963810 -3.483730 -3.517080 -2.724860 -1.405510
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+-4.159810 -4.945580 -4.784040 -3.764540 -2.959140
+-1.963850 -1.071260 -1.599580 -2.445320
+
+# 45
+-4.029070 -3.932660 -3.558480 -2.513980 -1.037320
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+-5.704430 -5.645660 -4.396040 -2.865450 -2.368170
+-2.860490 -3.416560 -3.666490 -3.859070
+
+# 60
+-3.338270 -2.960220 -2.311700 -1.272890 -0.246470
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+-2.041450 -3.218100 -3.915080 -4.852510 -5.696500
+-6.314370 -5.683690 -4.170620 -3.141000 -3.508820
+-3.756430 -3.640810 -3.640430 -3.550690
+
+# 75
+-2.244860 -1.632100 -1.000640 -0.170440 0.526440
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+-2.305650 -3.420580 -4.484960 -5.693140 -6.199150
+-6.253870 -5.211310 -4.174380 -3.685150 -4.151360
+-4.161970 -3.725150 -3.715310 -2.606760
+
+# 90
+-1.720840 -1.177830 -0.428430 0.277730 0.807900
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+-2.793220 -3.828560 -5.211800 -6.636850 -6.989940
+-6.108800 -5.452410 -3.911450 -4.321000 -4.587240
+-4.102610 -3.772820 -3.157300 -2.648390
+
+# 105
+-1.850640 -1.092420 -0.445020 0.128490 1.005520
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+-3.014400 -4.481110 -6.053510 -6.865400 -6.871130
+-5.728240 -3.912230 -4.802110 -5.034640 -4.715990
+-4.601080 -4.086220 -3.274630 -2.410940
+
+# 120
+-1.969230 -1.116650 -0.540250 -0.150330 0.763520
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+-3.366270 -5.008260 -6.124810 -7.034830 -6.724320
+-3.700200 -4.510620 -5.185650 -5.361620 -4.847490
+-4.444320 -4.004260 -3.415720 -2.751230
+
+# 135
+-2.111250 -1.168960 -0.322790 -0.006920 0.316660
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+-3.469470 -4.946030 -6.112560 -1.915580 -4.047310
+-4.996740 -4.996730 -4.842690 -4.886620 -4.300540
+-4.494620 -4.442210 -4.163570 -3.183510
+
+# 150
+-1.757590 -0.403620 0.023920 0.362390 0.634520
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+-3.152820 1.835120 -1.762860 -5.093660 -5.744830
+-5.390070 -4.783930 -4.190630 -4.115420 -4.042280
+-4.125570 -4.028550 -4.026100 -2.937910
+
+# 165
+-0.810590 -0.071500 0.378890 0.543310 1.277880
+1.641310 1.698840 1.519950 0.631950 -1.088670
+-2.736530 -0.735240 -4.563830 -6.408350 -5.889450
+-5.141750 -4.194970 -3.666490 -3.843450 -3.818830
+-3.826180 -3.596820 -2.994790 -2.231020
+
+#  proline, type 3
+
+#  -180.00
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+-7.18530 -7.63320 -8.41920 -9.12510 -8.97830
+-9.02750 -8.88890 -8.61060 -8.10240 -7.96680
+-7.98860 -7.96190 -7.56330 -7.73950 -8.31580
+-9.33380 -9.61880 -7.91860 -6.00570
+
+#  -165.00
+-3.21030 -2.90350 -3.04340 -3.83720 -4.92360
+-5.41790 -5.78320 -6.62490 -7.17820 -7.59500
+-7.60980 -7.39440 -6.68190 -6.24950 -5.83810
+-5.90510 -5.57900 -4.89950 -5.18840 -6.13180
+-6.93510 -7.49160 -5.84410 -4.48890
+
+#  -150.00
+-2.23750 -2.26520 -2.55120 -3.67610 -4.61620
+-5.01560 -5.36920 -5.93110 -6.16820 -6.48830
+-6.54220 -6.14310 -5.33350 -4.85090 -4.50790
+-4.44050 -4.34380 -4.13820 -4.35620 -5.24880
+-6.05280 -6.18610 -4.80390 -3.41730
+
+#  -135.00
+-2.12830 -2.02010 -2.90220 -3.88240 -4.63610
+-5.02000 -5.46090 -5.79830 -5.63220 -6.41490
+-6.20330 -5.57550 -4.58160 -4.15850 -4.00710
+-3.95020 -3.76880 -4.09690 -4.52680 -5.33410
+-5.97380 -5.68710 -4.70040 -3.33790
+
+#  -120.00
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+-4.57860 -4.95030 -5.23950 -5.37730 -6.14740
+-5.98660 -5.17760 -4.16090 -3.78450 -3.83210
+-3.86590 -4.21340 -4.26250 -4.16200 -4.62160
+-5.47440 -5.38280 -4.39100 -3.16760
+
+#  -105.00
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+-3.15410 -2.83060 -3.04980 -4.04810 -5.02030
+-4.84090 -3.88520 -2.79540 -2.49190 -2.65990
+-3.34670 -3.60580 -3.76970 -4.07430 -4.21930
+-4.66740 -4.23940 -3.37160 -2.10050
+
+#   -90.00
+-0.27400 -0.41780 -0.92340 -1.48470 -1.84370
+-1.42480 -1.14210 -1.83280 -2.97900 -3.57000
+-3.33310 -2.24200 -1.31350 -0.96640  0.38300
+-0.57540 -0.74080 -0.59130 -0.41960 -2.64120
+-3.25380 -2.85540 -2.09970 -0.95660
+
+#   -75.00
+ 0.26880  0.18190  0.00300 -0.45390 -0.24210
+ 0.21240  0.33320 -0.95520 -2.17670 -2.66490
+-2.24910 -1.35480 -0.35030  1.84000  0.81880
+ 0.41530  0.58460  0.65350  0.54960  0.41300
+ 0.23350 -2.13490 -1.54900 -0.38340
+
+#   -60.00
+-0.48820 -0.40730 -0.25210 -0.20490  0.53370
+ 1.05990  0.72540 -0.68300 -2.10190 -2.83530
+-2.55500 -1.33940 -0.24710  1.63190  1.10600
+ 1.16350  1.30720  1.49310  1.16160  0.99320
+-2.33360 -2.59380 -2.01110 -1.46840
+
+#   -45.00
+-2.41010 -1.30740 -0.85960 -0.06830  0.20500
+ 0.00650 -0.59750 -2.39820 -3.98270 -4.46610
+-3.51230 -1.99330  0.96050  0.80870  0.64450
+ 0.82590  1.00550  1.28110  0.96670 -2.71140
+-4.18330 -4.83370 -4.49950 -3.47920
+
+#   -30.00
+-3.46300 -2.06680 -0.84260 -0.70440 -1.85140
+-2.59990 -3.62600 -5.08050 -6.35480 -6.08340
+-4.78650 -1.24210 -0.81660 -0.60170 -0.50040
+-0.41020 -0.28450 -0.14620 -3.14950 -5.16280
+-6.81940 -7.52060 -7.12480 -5.49420
+
+#   -15.00
+-2.70550 -1.11410 -0.82120 -3.80470 -4.50780
+-4.64960 -5.78530 -7.04450 -7.30810 -6.56450
+-3.47860 -2.68630 -1.78120 -1.48400 -1.45930
+-1.43060 -5.75320 -2.72500 -6.45790 -8.16530
+-9.86330 -9.80710 -8.62670 -6.49690
+
+#     0.00
+-2.73190 -3.83060 -5.26960 -5.91610 -6.71690
+-7.05420 -7.77520 -7.81220 -7.54160 -4.98400
+-5.05070 -4.28910 -3.78740 -3.64600 -3.91990
+-3.55740 -3.03470 -5.78910 -7.02720 -8.04090
+-8.60950 -8.27740 -7.10120 -5.12040
+
+#    15.00
+-3.17420 -4.66830 -6.17790 -7.26760 -8.22560
+-8.32120 -7.64880 -7.00240 -4.77210 -5.65380
+-5.36790 -4.43640 -4.37720 -4.45280 -4.47980
+-4.07260 -6.75420 -7.56910 -7.95830 -7.87760
+-7.88160 -7.29010 -7.15600 -5.19260
+
+#    30.00
+-2.96240 -4.87720 -6.64930 -7.95180 -8.47610
+-7.49950 -6.26260 -6.35040 -4.34190 -4.49790
+-4.27480 -1.75620 -3.89990 -3.81400 -3.99610
+-6.66430 -7.66400 -7.80660 -7.21980 -6.83750
+-6.88220 -7.10200 -5.10200 -2.38920
+
+# 45
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
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+
+# 60
+0.000000 0.000000 0.000000 0.000000 0.000000
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+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
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+
+# 75
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 90
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 105
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 120
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 135
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 150
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 165
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000 0.000000
+0.000000 0.000000 0.000000 0.000000
+
+# 2 adjacent prolines, type 4
+
+#  -180.00
+-4.60660 -4.28920 -4.51420 -5.49210 -6.65460
+-7.18530 -7.63320 -8.41920 -9.12510 -8.97830
+-9.02750 -8.88890 -8.61060 -8.10240 -7.96680
+-7.98860 -7.96190 -7.56330 -7.73950 -8.31580
+-9.33380 -9.61880 -7.91860 -6.00570
+
+#  -165.00
+-3.21030 -2.90350 -3.04340 -3.83720 -4.92360
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+-5.716250 -4.434060 -2.788600 -0.974400 -0.729200
+-0.904940 -1.833540 -3.017700 -3.313450 -3.336010
+-3.181640 -3.594720 -1.231370 -0.603790 0.128810
+-1.222610 -0.909150 -0.837700 -1.346820 -3.040880
+-4.731110 -5.844860 -6.428460 -6.424880
+
+# -15
+-3.991110 -2.046000 0.082550 -2.676110 -2.828500
+-2.596640 -2.843330 -3.011480 -2.312640 -2.405980
+-3.086210 -1.164620 -1.231660 -0.871900 -0.348980
+-1.735900 -0.914150 -0.484520 -1.818040 -3.602550
+-5.330320 -5.992270 -5.588080 -5.408360
+
+# 0
+-1.147060 -3.317730 -4.305100 -4.615200 -4.533780
+-3.622950 -2.832800 -1.872810 -1.144300 -1.994070
+-0.741980 -1.115010 -1.229250 -1.103680 -0.742430
+-1.973970 -1.070020 -1.802220 -2.712770 -3.624130
+-4.537100 -4.619970 -4.310890 -3.318290
+
+# 15
+-3.997710 -5.408360 -5.588080 -5.992270 -5.330320
+-3.602550 -1.818040 -0.484520 -0.914150 -1.735900
+-0.348980 -0.871900 -1.231660 -1.164620 -3.086210
+-2.405980 -2.312640 -3.011480 -2.843330 -2.596640
+-2.828500 -2.676110 0.082550 -2.046000
+
+# 30
+-5.710850 -6.424880 -6.428460 -5.844860 -4.731110
+-3.040880 -1.346820 -0.837700 -0.909150 -1.222610
+0.128810 -0.603790 -1.231370 -3.594720 -3.181640
+-3.336010 -3.313450 -3.017700 -1.833540 -0.904940
+-0.729200 -0.974400 -2.788600 -4.434060
+
+# 45
+-6.754940 -6.613030 -6.128530 -5.207530 -4.094860
+-2.751370 -1.561900 -1.121840 -0.925490 -1.455400
+-2.112940 -3.009910 -3.688580 -3.735160 -4.237410
+-4.558570 -3.892650 -2.037170 -0.536700 -0.526660
+-1.708710 -2.714090 -4.362190 -5.850030
+
+# 60
+-6.188070 -5.565810 -4.821040 -4.008100 -2.948140
+-2.431360 -1.337310 -1.002930 -0.877560 -1.453990
+-2.495430 -3.374140 -3.796280 -4.666260 -4.993340
+-3.687830 -2.962910 -1.119790 -1.094850 -2.067520
+-2.683230 -4.000820 -4.878940 -5.456080
+
+# 75
+-4.986080 -3.970600 -3.347950 -2.659400 -1.892510
+-1.607440 -1.312730 -1.269930 -0.756620 -1.859410
+-2.986660 -3.675410 -5.708500 -5.536170 -4.492140
+-3.715530 -1.945510 -1.105500 -1.664160 -2.345360
+-3.228630 -3.892550 -4.485310 -4.995210
+
+# 90
+-3.879190 -2.939990 -2.420970 -1.794480 -1.141350
+-1.020680 -1.065550 -0.971340 -1.139090 -1.898510
+-2.864390 -4.359900 -5.446890 -4.981430 -4.181160
+-2.808170 -0.971860 -1.452040 -1.975250 -2.406460
+-3.040850 -3.611370 -3.902110 -3.713610
+
+# 105
+-2.793280 -2.412680 -1.959970 -1.401500 -0.950190
+-0.540540 -0.467320 -0.633810 -0.893140 -1.695490
+-2.776760 -4.255190 -4.662850 -4.448210 -3.332800
+-2.567680 -1.195390 -1.681850 -1.951490 -2.266680
+-2.626630 -3.013710 -3.178150 -3.079570
+
+# 120
+-2.330190 -1.914850 -1.601800 -1.068330 -0.661220
+-0.297950 -0.173830 -0.158900 -0.553910 -1.455320
+-2.394430 -3.215190 -3.975820 -3.783210 -3.014390
+-0.975570 -1.358170 -1.289220 -1.435540 -1.705860
+-1.970070 -2.364070 -2.596140 -2.593790
+
+# 135
+-1.796120 -1.465530 -1.267450 -0.880610 -0.288370
+-0.055650 0.100910 -0.207560 -0.758950 -1.718060
+-2.220710 -2.435890 -4.372310 0.338010 -1.062570
+-1.337360 -1.020630 -0.851590 -0.801350 -0.886880
+-1.567160 -1.803720 -2.143020 -2.117750
+
+# 150
+-1.263610 -0.710760 -0.794980 -0.563330 -0.339050
+-0.092820 0.033160 0.000490 -0.628990 -1.664160
+-2.225630 -2.949180 0.753400 -1.546500 -2.165440
+-1.626260 -0.887080 -0.290670 -0.054220 -1.642540
+-1.119780 -1.656770 -1.665900 -1.482430
+
+# 165
+-0.684660 -0.477660 -0.348750 -0.462500 -0.271890
+-0.000430 0.196710 0.180860 -0.410680 -1.810120
+-2.675640 1.822690 -1.636020 -3.153350 -2.780320
+-1.715700 -0.534910 0.258100 0.329180 -0.126160
+-0.940260 -1.319240 -0.990850 -0.896700
+
diff --git a/examples/cmap/gagg.data b/examples/cmap/gagg.data
new file mode 100644
index 0000000000..fd2aa193c4
--- /dev/null
+++ b/examples/cmap/gagg.data
@@ -0,0 +1,380 @@
+Created by charmm2lammps v1.8.2.6 beta on Sun Mar 20 00:26:35 EDT 2016
+
+          34  atoms
+          33  bonds
+          57  angles
+          75  dihedrals
+           7  impropers
+           2  crossterms
+
+          13  atom types
+          15  bond types
+          30  angle types
+          42  dihedral types
+           5  improper types
+
+  -34.414709    45.585291 xlo xhi
+  -36.134827    43.865173 ylo yhi
+  -39.349142    40.650858 zlo zhi
+
+Masses
+
+       1      1.008  # H
+       2      1.008  # HC
+       3      1.008  # HA
+       4      1.008  # HB
+       5     12.011  # C
+       6     12.011  # CT1
+       7     12.011  # CT2
+       8     12.011  # CT3
+       9     12.011  # CC
+      10     14.007  # NH1
+      11     14.007  # NH3
+      12     15.999  # O
+      13     15.999  # OC
+
+Pair Coeffs
+
+       1            0.046   0.400013524445            0.046   0.400013524445  # H
+       2            0.046   0.400013524445            0.046   0.400013524445  # HC
+       3            0.022    2.35197261589            0.022    2.35197261589  # HA
+       4            0.022    2.35197261589            0.022    2.35197261589  # HB
+       5             0.11    3.56359487256             0.11    3.56359487256  # C
+       6             0.02    4.05358916754             0.01    3.38541512893  # CT1
+       7            0.055    3.87540942391             0.01    3.38541512893  # CT2
+       8             0.08    3.67050271874             0.01    3.38541512893  # CT3
+       9             0.07    3.56359487256             0.07    3.56359487256  # CC
+      10              0.2    3.29632525712              0.2    2.76178602624  # NH1
+      11              0.2    3.29632525712              0.2    3.29632525712  # NH3
+      12             0.12    3.02905564168             0.12    2.49451641079  # O
+      13             0.12    3.02905564168             0.12    3.02905564168  # OC
+
+Atoms
+
+       1       1    11      -0.3     0.0088076654    -0.0395361015    -0.0125765907  # NH3
+       2       1     2      0.33    -0.3781208354    -1.0038773849      -0.01724272  # HC
+       3       1     2      0.33    -0.3448285543     0.4901827566    -0.8403800387  # HC
+       4       1     2      0.33    -0.3306420078     0.4732826156     0.8294424358  # HC
+       5       1     7      0.13      1.526230489    -0.0164860529    -0.0402820599  # CT2
+       6       1     4      0.09     1.8596639218    -0.5263587482    -0.9333647137  # HB
+       7       1     4      0.09     1.8904342902    -0.4510777655     0.8809945249  # HB
+       8       1     5      0.51     2.0135471936     1.4020233344    -0.1137107587  # C
+       9       1    12     -0.51     1.1818164992     2.2781068718     -0.313197467  # O
+      10       2    10     -0.47     3.3194424268      1.666672014     0.0713249543  # NH1
+      11       2     1      0.31     4.0409429153     0.9783582555     0.1693897169  # H
+      12       2     6      0.07     3.8529467728     3.0161771739     0.0690818527  # CT1
+      13       2     4      0.09     3.5315723829     3.5134434764    -0.8378950509  # HB
+      14       2     8     -0.27     3.3981217437     3.8178727883     1.3071600161  # CT3
+      15       2     3      0.09     2.2921877645     3.9163330652     1.3111957959  # HA
+      16       2     3      0.09     3.7142964083     3.3104118688     2.2424399743  # HA
+      17       2     3      0.09     3.8238672849     4.8446179852     1.2978564897  # HA
+      18       2     5      0.51     5.3731873136      2.946062408     0.0042414688  # C
+      19       2    12     -0.51     5.9268816775     1.8488403755     0.0011766847  # O
+      20       3    10     -0.47     6.0445386951     4.1111769168    -0.0636349698  # NH1
+      21       3     1      0.31     5.5768514013     4.9972489389    -0.0653583036  # H
+      22       3     7     -0.02     7.4911642129     4.2772062416    -0.0346088891  # CT2
+      23       3     4      0.09     7.9218377956     3.8786283786    -0.9407244447  # HB
+      24       3     4      0.09     7.8877470687     3.8607990619     0.8803359097  # HB
+      25       3     5      0.51     7.7351287723     5.7597169026    -0.0088736611  # C
+      26       3    12     -0.51     6.7657462979     6.5189223559      0.005150418  # O
+      27       4    10     -0.47     9.0014031015     6.1940849758    -0.0045995102  # NH1
+      28       4     1      0.31     9.8272711181     5.6225413025     -0.008448093  # H
+      29       4     7     -0.02     9.4067557288     7.5845263022     0.0016383819  # CT2
+      30       4     4      0.09     9.0736276253     8.0578903151     0.9119901724  # HB
+      31       4     4      0.09     9.0736165596      8.064051906    -0.9055419386  # HB
+      32       4     9      0.34    10.9382207556      7.612479283     0.0008762597  # CC
+      33       4    13     -0.67    11.5487033003     6.5062943609    -0.0007524693  # OC
+      34       4    13     -0.67    11.5055524841      8.734223435     0.0013684148  # OC
+
+Bond Coeffs
+
+       1              250             1.49  # C    CT1 
+       2              250             1.49  # C    CT2 
+       3              370            1.345  # C    NH1 
+       4              620             1.23  # C    O   
+       5              200            1.522  # CC   CT2 
+       6              525             1.26  # CC   OC  
+       7            222.5            1.538  # CT1  CT3 
+       8              330             1.08  # CT1  HB  
+       9              320             1.43  # CT1  NH1 
+      10              330             1.08  # CT2  HB  
+      11              320             1.43  # CT2  NH1 
+      12              200             1.48  # CT2  NH3 
+      13              322            1.111  # CT3  HA  
+      14              440            0.997  # H    NH1 
+      15              403             1.04  # HC   NH3 
+
+Bonds
+
+       1      15       2       1  # HC   NH3 
+       2      15       3       1  # HC   NH3 
+       3      15       4       1  # HC   NH3 
+       4      12       1       5  # CT2  NH3 
+       5       2       8       5  # C    CT2 
+       6       3       8      10  # C    NH1 
+       7      10       5       6  # CT2  HB  
+       8      10       5       7  # CT2  HB  
+       9       4       9       8  # C    O   
+      10       7      14      12  # CT1  CT3 
+      11      14      10      11  # H    NH1 
+      12       9      10      12  # CT1  NH1 
+      13       1      18      12  # C    CT1 
+      14       3      18      20  # C    NH1 
+      15       8      12      13  # CT1  HB  
+      16      13      14      15  # CT3  HA  
+      17      13      14      16  # CT3  HA  
+      18      13      14      17  # CT3  HA  
+      19       4      19      18  # C    O   
+      20      14      20      21  # H    NH1 
+      21      11      20      22  # CT2  NH1 
+      22       2      25      22  # C    CT2 
+      23       3      25      27  # C    NH1 
+      24      10      22      23  # CT2  HB  
+      25      10      22      24  # CT2  HB  
+      26       4      26      25  # C    O   
+      27      14      27      28  # H    NH1 
+      28      11      27      29  # CT2  NH1 
+      29       5      32      29  # CC   CT2 
+      30      10      29      30  # CT2  HB  
+      31      10      29      31  # CT2  HB  
+      32       6      32      34  # CC   OC  
+      33       6      32      33  # CC   OC  
+
+Angle Coeffs
+
+       1               52              108                0                0  # C    CT1  CT3 
+       2               50            109.5                0                0  # C    CT1  HB  
+       3               50              107                0                0  # C    CT1  NH1 
+       4               50            109.5                0                0  # C    CT2  HB  
+       5               50              107                0                0  # C    CT2  NH1 
+       6             43.7              110                0                0  # C    CT2  NH3 
+       7               50              120                0                0  # C    NH1  CT1 
+       8               50              120                0                0  # C    NH1  CT2 
+       9               34              123                0                0  # C    NH1  H   
+      10               50            109.5                0                0  # CC   CT2  HB  
+      11               50              107                0                0  # CC   CT2  NH1 
+      12               80            116.5                0                0  # CT1  C    NH1 
+      13               80              121                0                0  # CT1  C    O   
+      14            33.43            110.1            22.53            2.179  # CT1  CT3  HA  
+      15               35              117                0                0  # CT1  NH1  H   
+      16               80            116.5                0                0  # CT2  C    NH1 
+      17               80              121                0                0  # CT2  C    O   
+      18               40              118               50            2.388  # CT2  CC   OC  
+      19               35              117                0                0  # CT2  NH1  H   
+      20               30            109.5               20            2.074  # CT2  NH3  HC  
+      21               35              111                0                0  # CT3  CT1  HB  
+      22               70            113.5                0                0  # CT3  CT1  NH1 
+      23             35.5            108.4              5.4            1.802  # HA   CT3  HA  
+      24               48              108                0                0  # HB   CT1  NH1 
+      25               36              115                0                0  # HB   CT2  HB  
+      26               48              108                0                0  # HB   CT2  NH1 
+      27             51.5            107.5                0                0  # HB   CT2  NH3 
+      28               44            109.5                0                0  # HC   NH3  HC  
+      29               80            122.5                0                0  # NH1  C    O   
+      30              100              124               70            2.225  # OC   CC   OC  
+
+Angles
+
+       1      28       2       1       3  # HC   NH3  HC  
+       2      28       2       1       4  # HC   NH3  HC  
+       3      20       2       1       5  # CT2  NH3  HC  
+       4      28       3       1       4  # HC   NH3  HC  
+       5      20       3       1       5  # CT2  NH3  HC  
+       6      20       4       1       5  # CT2  NH3  HC  
+       7      27       1       5       6  # HB   CT2  NH3 
+       8      27       1       5       7  # HB   CT2  NH3 
+       9       6       1       5       8  # C    CT2  NH3 
+      10      25       6       5       7  # HB   CT2  HB  
+      11       4       6       5       8  # C    CT2  HB  
+      12       4       7       5       8  # C    CT2  HB  
+      13      17       5       8       9  # CT2  C    O   
+      14      16       5       8      10  # CT2  C    NH1 
+      15      29       9       8      10  # NH1  C    O   
+      16       9       8      10      11  # C    NH1  H   
+      17       7       8      10      12  # C    NH1  CT1 
+      18      15      11      10      12  # CT1  NH1  H   
+      19      24      10      12      13  # HB   CT1  NH1 
+      20      22      10      12      14  # CT3  CT1  NH1 
+      21       3      10      12      18  # C    CT1  NH1 
+      22      21      13      12      14  # CT3  CT1  HB  
+      23       2      13      12      18  # C    CT1  HB  
+      24       1      14      12      18  # C    CT1  CT3 
+      25      14      12      14      15  # CT1  CT3  HA  
+      26      14      12      14      16  # CT1  CT3  HA  
+      27      14      12      14      17  # CT1  CT3  HA  
+      28      23      15      14      16  # HA   CT3  HA  
+      29      23      15      14      17  # HA   CT3  HA  
+      30      23      16      14      17  # HA   CT3  HA  
+      31      13      12      18      19  # CT1  C    O   
+      32      12      12      18      20  # CT1  C    NH1 
+      33      29      19      18      20  # NH1  C    O   
+      34       9      18      20      21  # C    NH1  H   
+      35       8      18      20      22  # C    NH1  CT2 
+      36      19      21      20      22  # CT2  NH1  H   
+      37      26      20      22      23  # HB   CT2  NH1 
+      38      26      20      22      24  # HB   CT2  NH1 
+      39       5      20      22      25  # C    CT2  NH1 
+      40      25      23      22      24  # HB   CT2  HB  
+      41       4      23      22      25  # C    CT2  HB  
+      42       4      24      22      25  # C    CT2  HB  
+      43      17      22      25      26  # CT2  C    O   
+      44      16      22      25      27  # CT2  C    NH1 
+      45      29      26      25      27  # NH1  C    O   
+      46       9      25      27      28  # C    NH1  H   
+      47       8      25      27      29  # C    NH1  CT2 
+      48      19      28      27      29  # CT2  NH1  H   
+      49      26      27      29      30  # HB   CT2  NH1 
+      50      26      27      29      31  # HB   CT2  NH1 
+      51      11      27      29      32  # CC   CT2  NH1 
+      52      25      30      29      31  # HB   CT2  HB  
+      53      10      30      29      32  # CC   CT2  HB  
+      54      10      31      29      32  # CC   CT2  HB  
+      55      18      29      32      33  # CT2  CC   OC  
+      56      18      29      32      34  # CT2  CC   OC  
+      57      30      33      32      34  # OC   CC   OC  
+
+Dihedral Coeffs
+
+       1              0.2                3                0                1  # C    CT1  CT3  HA  
+       2              0.2                1              180                1  # C    CT1  NH1  C   
+       3                0                1                0                1  # C    CT1  NH1  H   
+       4              0.2                1              180                1  # C    CT2  NH1  C   
+       5                0                1                0                1  # C    CT2  NH1  H   
+       6              0.1                3                0                1  # C    CT2  NH3  HC  
+       7              1.8                1                0                1  # C    NH1  CT1  CT3 
+       8                0                1                0                1  # C    NH1  CT1  HB  
+       9              0.2                1              180                1  # C    NH1  CT2  CC  
+      10                0                1                0                1  # C    NH1  CT2  HB  
+      11                0                1                0                1  # CC   CT2  NH1  H   
+      12              1.6                1                0                1  # CT1  C    NH1  CT2 
+      13              2.5                2              180                0  # CT1  C    NH1  CT2 
+      14              2.5                2              180                1  # CT1  C    NH1  H   
+      15              1.6                1                0                1  # CT1  NH1  C    CT2 
+      16              2.5                2              180                0  # CT1  NH1  C    CT2 
+      17              2.5                2              180                1  # CT1  NH1  C    O   
+      18              1.6                1                0                1  # CT2  C    NH1  CT2 
+      19              2.5                2              180                0  # CT2  C    NH1  CT2 
+      20              2.5                2              180                1  # CT2  C    NH1  H   
+      21              2.5                2              180                1  # CT2  NH1  C    O   
+      22                0                1                0                1  # CT3  CT1  C    NH1 
+      23              1.4                1                0                1  # CT3  CT1  C    O   
+      24                0                1                0                1  # CT3  CT1  NH1  H   
+      25              2.5                2              180                1  # H    NH1  C    O   
+      26                0                1                0                1  # H    NH1  CT1  HB  
+      27                0                1                0                1  # H    NH1  CT2  HB  
+      28              0.2                3                0                1  # HA   CT3  CT1  HB  
+      29              0.2                3                0                1  # HA   CT3  CT1  NH1 
+      30                0                1                0                1  # HB   CT1  C    NH1 
+      31                0                1                0                1  # HB   CT1  C    O   
+      32                0                1                0                1  # HB   CT2  C    NH1 
+      33                0                1                0                1  # HB   CT2  C    O   
+      34             0.05                6              180                1  # HB   CT2  CC   OC  
+      35              0.1                3                0                1  # HB   CT2  NH3  HC  
+      36              0.6                1                0                1  # NH1  C    CT1  NH1 
+      37              0.6                1                0                1  # NH1  C    CT2  NH1 
+      38              0.4                1                0                1  # NH1  C    CT2  NH3 
+      39                0                1                0                1  # NH1  CT1  C    O   
+      40                0                1                0                1  # NH1  CT2  C    O   
+      41             0.05                6              180                1  # NH1  CT2  CC   OC  
+      42                0                1                0                1  # NH3  CT2  C    O   
+
+Dihedrals
+
+       1      42       1       5       8       9  # NH3  CT2  C    O   
+       2      38       1       5       8      10  # NH1  C    CT2  NH3 
+       3      35       2       1       5       6  # HB   CT2  NH3  HC  
+       4      35       2       1       5       7  # HB   CT2  NH3  HC  
+       5       6       2       1       5       8  # C    CT2  NH3  HC  
+       6      35       3       1       5       6  # HB   CT2  NH3  HC  
+       7      35       3       1       5       7  # HB   CT2  NH3  HC  
+       8       6       3       1       5       8  # C    CT2  NH3  HC  
+       9      35       4       1       5       6  # HB   CT2  NH3  HC  
+      10      35       4       1       5       7  # HB   CT2  NH3  HC  
+      11       6       4       1       5       8  # C    CT2  NH3  HC  
+      12      20       5       8      10      11  # CT2  C    NH1  H   
+      13      15       5       8      10      12  # CT1  NH1  C    CT2 
+      14      16       5       8      10      12  # CT1  NH1  C    CT2 
+      15      33       6       5       8       9  # HB   CT2  C    O   
+      16      32       6       5       8      10  # HB   CT2  C    NH1 
+      17      33       7       5       8       9  # HB   CT2  C    O   
+      18      32       7       5       8      10  # HB   CT2  C    NH1 
+      19       8       8      10      12      13  # C    NH1  CT1  HB  
+      20       7       8      10      12      14  # C    NH1  CT1  CT3 
+      21       2       8      10      12      18  # C    CT1  NH1  C   
+      22      25       9       8      10      11  # H    NH1  C    O   
+      23      17       9       8      10      12  # CT1  NH1  C    O   
+      24      29      10      12      14      15  # HA   CT3  CT1  NH1 
+      25      29      10      12      14      16  # HA   CT3  CT1  NH1 
+      26      29      10      12      14      17  # HA   CT3  CT1  NH1 
+      27      39      10      12      18      19  # NH1  CT1  C    O   
+      28      36      10      12      18      20  # NH1  C    CT1  NH1 
+      29      26      11      10      12      13  # H    NH1  CT1  HB  
+      30      24      11      10      12      14  # CT3  CT1  NH1  H   
+      31       3      11      10      12      18  # C    CT1  NH1  H   
+      32      14      12      18      20      21  # CT1  C    NH1  H   
+      33      12      12      18      20      22  # CT1  C    NH1  CT2 
+      34      13      12      18      20      22  # CT1  C    NH1  CT2 
+      35      28      13      12      14      15  # HA   CT3  CT1  HB  
+      36      28      13      12      14      16  # HA   CT3  CT1  HB  
+      37      28      13      12      14      17  # HA   CT3  CT1  HB  
+      38      31      13      12      18      19  # HB   CT1  C    O   
+      39      30      13      12      18      20  # HB   CT1  C    NH1 
+      40      23      14      12      18      19  # CT3  CT1  C    O   
+      41      22      14      12      18      20  # CT3  CT1  C    NH1 
+      42       1      15      14      12      18  # C    CT1  CT3  HA  
+      43       1      16      14      12      18  # C    CT1  CT3  HA  
+      44       1      17      14      12      18  # C    CT1  CT3  HA  
+      45      10      18      20      22      23  # C    NH1  CT2  HB  
+      46      10      18      20      22      24  # C    NH1  CT2  HB  
+      47       4      18      20      22      25  # C    CT2  NH1  C   
+      48      25      19      18      20      21  # H    NH1  C    O   
+      49      21      19      18      20      22  # CT2  NH1  C    O   
+      50      40      20      22      25      26  # NH1  CT2  C    O   
+      51      37      20      22      25      27  # NH1  C    CT2  NH1 
+      52      27      21      20      22      23  # H    NH1  CT2  HB  
+      53      27      21      20      22      24  # H    NH1  CT2  HB  
+      54       5      21      20      22      25  # C    CT2  NH1  H   
+      55      20      22      25      27      28  # CT2  C    NH1  H   
+      56      18      22      25      27      29  # CT2  C    NH1  CT2 
+      57      19      22      25      27      29  # CT2  C    NH1  CT2 
+      58      33      23      22      25      26  # HB   CT2  C    O   
+      59      32      23      22      25      27  # HB   CT2  C    NH1 
+      60      33      24      22      25      26  # HB   CT2  C    O   
+      61      32      24      22      25      27  # HB   CT2  C    NH1 
+      62      10      25      27      29      30  # C    NH1  CT2  HB  
+      63      10      25      27      29      31  # C    NH1  CT2  HB  
+      64       9      25      27      29      32  # C    NH1  CT2  CC  
+      65      25      26      25      27      28  # H    NH1  C    O   
+      66      21      26      25      27      29  # CT2  NH1  C    O   
+      67      41      27      29      32      33  # NH1  CT2  CC   OC  
+      68      41      27      29      32      34  # NH1  CT2  CC   OC  
+      69      27      28      27      29      30  # H    NH1  CT2  HB  
+      70      27      28      27      29      31  # H    NH1  CT2  HB  
+      71      11      28      27      29      32  # CC   CT2  NH1  H   
+      72      34      30      29      32      33  # HB   CT2  CC   OC  
+      73      34      30      29      32      34  # HB   CT2  CC   OC  
+      74      34      31      29      32      33  # HB   CT2  CC   OC  
+      75      34      31      29      32      34  # HB   CT2  CC   OC  
+
+Improper Coeffs
+
+       1              120                0  # C    CT1  NH1  O   
+       2              120                0  # C    CT2  NH1  O   
+       3               96                0  # CC   CT2  OC   OC  
+       4               20                0  # H    CT1  C    NH1 
+       5               20                0  # H    CT2  C    NH1 
+
+Impropers
+
+       1       2       8       5      10       9  # C    CT2  NH1  O   
+       2       4      10       8      12      11  # H    CT1  C    NH1 
+       3       1      18      12      20      19  # C    CT1  NH1  O   
+       4       5      20      18      22      21  # H    CT2  C    NH1 
+       5       2      25      22      27      26  # C    CT2  NH1  O   
+       6       5      27      25      29      28  # H    CT2  C    NH1 
+       7       3      32      29      34      33  # CC   CT2  OC   OC  
+
+CMAP
+
+       1       1       8      10      12      18      20
+       2       5      18      20      22      25      27
diff --git a/examples/cmap/in.cmap b/examples/cmap/in.cmap
new file mode 100644
index 0000000000..d2b2714b82
--- /dev/null
+++ b/examples/cmap/in.cmap
@@ -0,0 +1,36 @@
+# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016
+
+units           real
+neigh_modify    delay 2 every 1
+#newton          off
+
+boundary        p p p
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/charmm 8 12
+#pair_style      lj/charmmfsw/coul/charmmfsh 8 12
+pair_modify     mix arithmetic
+
+fix             cmap all cmap charmm22.cmap
+fix_modify      cmap energy yes
+
+read_data       gagg.data fix cmap crossterm CMAP
+
+special_bonds   charmm
+fix             1 all nve
+
+#fix             1 all nvt temp 300 300 100.0
+#fix             2 all shake 1e-9 500 0 m 1.0
+
+velocity        all create 0.0 12345678 dist uniform
+
+thermo          1000
+thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp
+timestep        2.0
+
+run             100000
diff --git a/examples/cmap/log.23Sep16.cmap.g++.1 b/examples/cmap/log.23Sep16.cmap.g++.1
new file mode 100644
index 0000000000..fe6caed913
--- /dev/null
+++ b/examples/cmap/log.23Sep16.cmap.g++.1
@@ -0,0 +1,200 @@
+LAMMPS (21 Sep 2016)
+# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016
+
+units           real
+neigh_modify    delay 2 every 1
+#newton          off
+
+boundary        p p p
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/charmm 8 12
+#pair_style      lj/charmmfsw/coul/charmmfsh 8 12
+pair_modify     mix arithmetic
+
+fix             cmap all cmap charmm22.cmap
+fix_modify      cmap energy yes
+
+read_data       gagg.data fix cmap crossterm CMAP
+  orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  34 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  12 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  33 bonds
+  reading angles ...
+  57 angles
+  reading dihedrals ...
+  75 dihedrals
+  reading impropers ...
+  7 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  13 = max # of 1-4 neighbors
+  16 = max # of special neighbors
+
+special_bonds   charmm
+fix             1 all nve
+
+#fix             1 all nvt temp 300 300 100.0
+#fix             2 all shake 1e-9 500 0 m 1.0
+
+velocity        all create 0.0 12345678 dist uniform
+
+thermo          1000
+thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp
+timestep        2.0
+
+run             100000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7 -> bins = 12 12 12
+Memory usage per processor = 14.6355 Mbytes
+Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro 
+       0    26.542777  -0.93822087    1.2470497    4.8441789    4.5432816    -1.473352   0.10453023 
+    1000    28.673005  -0.47724367   0.80029132     3.151679    4.4684446   -2.3928648   0.18604953 
+    2000     27.67955    -1.170342   0.72018905    4.0400131    4.4713764   -2.5490207   0.21834436 
+    3000    29.256656  -0.35856055   0.73303546    3.7411606    4.4710568   -2.8939692   0.37728884 
+    4000    30.097549   -1.1353905   0.79007053    3.0688444    4.4091469   -2.3383587   0.20743631 
+    5000    28.357525   -1.0723742    0.9180297    3.6579424    4.8792664   -2.3185572  0.088366962 
+    6000    29.214175  -0.95299225   0.81926009    3.6805429    4.6742897   -2.9343577   0.26697813 
+    7000    27.018614  -0.52423475   0.72502764    3.8840137    4.7780956   -2.3916009   0.24952584 
+    8000    29.682167   -1.0939711   0.76111486    3.1090116    4.9359719   -2.5662984    0.1411154 
+    9000    27.909695  -0.80905986   0.78952533     4.203187    4.1301204    -2.000402  0.088859259 
+   10000    27.480298  -0.86273377    1.1293962    4.3857421     4.899282   -3.3895621   0.12126215 
+   11000    28.303203   -1.0221152   0.62762348     4.055414    4.5863024   -2.5842816   0.17996907 
+   12000    28.311127  -0.94227367   0.91859012    3.6673926    4.7018632    -3.902715   0.30065704 
+   13000    30.818607   -1.5220116   0.95710386    3.3364371     4.543427   -3.0423067   0.16712905 
+   14000    27.643736   -1.0144117   0.95806952    4.1046912     4.800236   -4.0534389   0.29293405 
+   15000    27.660491   -1.0390086   0.78061056    4.1139174    4.7197202   -2.3670379   0.22126985 
+   16000    27.845157  -0.63654502   0.78007478    3.9365994     4.949418   -3.1470214   0.22335355 
+   17000     28.44772   -1.0255112   0.70402007    4.0573343    4.2887527   -2.2099596  0.048050962 
+   18000    27.128323  -0.96218536    1.1327159    4.3222585     4.326607   -2.2881766   0.13491257 
+   19000    27.337633  -0.78999574   0.80152298    4.2239689    4.7073478   -2.2924164   0.12710292 
+   20000    27.780537  -0.46458072   0.79707671    3.7232618     4.943417   -2.5290628   0.26191223 
+   21000    26.435484   -0.7803224    1.0753217    4.4196051    5.9945933   -2.3340925   0.16448475 
+   22000    28.619429   -1.1623149    0.9401731    3.8508844    5.1636737   -2.5551846   0.25318434 
+   23000    28.399338  -0.79700962   0.85575503     4.488526    4.5975422   -2.5663549   0.13601693 
+   24000    29.645532    -1.158744   0.83180313    3.8193399      4.60319   -2.6847864   0.24260466 
+   25000    28.695339   -1.4802204   0.76583757    3.6786272    4.8959496   -2.3627896  0.080867326 
+   26000    28.149711    -1.029689   0.79383806    3.7885067    4.3345813   -2.1041553   0.14598209 
+   27000    29.580373   -1.0525813    1.0262723    3.7767318    4.6119758   -2.2802386  0.088556038 
+   28000     28.44308  -0.93411225    0.8794395     3.948079     4.780246   -2.1814583   0.14340149 
+   29000    29.335621   -1.6087988   0.71803091    3.7819186    4.6688385   -2.4282242   0.16061111 
+   30000    28.706138   -1.3938241   0.67713818     4.031275    4.4756505   -2.1807056   0.11461356 
+   31000    27.451944  0.010297225   0.65064883    3.6402029    4.3607811   -2.5511516   0.12637237 
+   32000    27.070878    -1.103158    1.1932199    5.1329709    4.5201653   -2.2224479   0.11215427 
+   33000    29.889976   -1.6228316   0.69407996    3.5361991    4.3502767   -1.9847454   0.09089949 
+   34000    28.223151    -0.927208     1.043253    3.4650939    5.1028142   -2.8127219   0.10648823 
+   35000    27.985986  -0.48153861   0.63878449    3.3724641    4.9551679   -2.6565919   0.12123115 
+   36000    28.580688   -1.4500694     1.055762    4.0490064     4.423782   -2.3103578  0.072747638 
+   37000    29.192947  -0.49678176    1.1146731    2.9233947    4.5738603   -2.4376144   0.22874047 
+   38000    26.954594  -0.53812359   0.79230685    4.3356989    5.0284656   -2.3791255    0.0486081 
+   39000    27.567555  -0.57870028   0.73614374     4.191991    4.9209556   -2.6122044   0.08635571 
+   40000    28.494172  -0.79057135   0.79072816    4.1893209    4.4826919   -2.4179635   0.14612898 
+   41000     28.44904   -1.1002948   0.93405654    4.3586358    4.4338415   -2.2950944   0.15705834 
+   42000     28.95725   -1.0297067    1.1632348     4.274711    4.9979487   -2.7611464   0.15944725 
+   43000    28.640394  -0.70938882   0.68100893    3.1844315    5.1817454   -2.2837487   0.14189233 
+   44000    27.997558   -1.0115099   0.59125208    4.0883422    4.6033907   -2.2775964  0.094273258 
+   45000     27.67163  -0.67992747    1.1225552    3.9020703    4.8171056   -2.1952679  0.041418433 
+   46000    28.822607   -0.6687953   0.74160059    3.3193715    4.5546965   -2.3024572  0.047569065 
+   47000     29.20147   -1.4456785   0.79223353    3.8288813    4.5811826   -2.5154936  0.061230141 
+   48000    27.843026   -1.0222301   0.87322137    4.3432743    4.4266307   -2.1414153   0.06802794 
+   49000    28.199573   -1.1887794    1.2781088    4.0779644    4.5881353    -2.319775  0.094803547 
+   50000    28.759212    -1.354416   0.68534569    3.8394841    4.2308134   -2.1281844    0.1395951 
+   51000    27.876455   -1.5705462   0.76557156    4.5335223     4.523708    -2.203702   0.14679803 
+   52000    27.930587   -1.2277489   0.96071516     3.960953    5.1152188   -2.4101451  0.060949521 
+   53000    27.031236   -1.4746477    1.2341141    5.0540975    4.3656865   -2.1288513  0.092725656 
+   54000    28.809394   -1.1162427   0.94350207    3.4013958    4.4755547   -2.3342811   0.18855912 
+   55000    28.948415   -1.1560418    0.6260139    3.5386373    4.5244978    -2.340212   0.17474657 
+   56000    28.048368  -0.95784532   0.76432571    4.1404665    4.4570033   -2.0899628  0.045693628 
+   57000    28.707642    -1.366574    0.9907873     3.729903    4.3131997   -2.2777698  0.065420213 
+   58000    26.361663   -1.0424403    1.0452563    5.0977108    4.7035231   -2.3101244   0.13671642 
+   59000    29.218218   -1.2210564   0.62435875    3.4236327    4.5481681   -2.1575943  0.037984042 
+   60000    27.655546   -1.1053224   0.86323501    3.7641375    4.8946898   -2.2422249  0.077725979 
+   61000    27.252108   -1.3744824    1.1150806    5.0444848    4.4878135   -2.2743829  0.058331257 
+   62000    27.163469   -1.1715781   0.72099321    4.5295501    4.9509918   -2.2993961  0.050401105 
+   63000    29.581575   -1.2238537   0.86303245    3.1194038    5.2218965   -2.5002427  0.055032632 
+   64000    27.897822   -1.1011516   0.74540883    4.2869228    4.3394269   -2.2552393    0.1403321 
+   65000    27.083245   -1.0633392   0.92771724    5.0805224    4.2747962   -2.2388039  0.064196692 
+   66000    29.072723   -1.5514209   0.89798805    4.2600224    4.4261812   -2.3524752   0.15067414 
+   67000    27.308181  -0.72224802   0.97109517    4.5074578    4.4559352   -2.1381121  0.089297603 
+   68000    27.505686  -0.43855431   0.80785812    4.1917251    5.0157721   -2.3382145   0.11105164 
+   69000    29.041681  -0.64735378   0.89874684    3.3891579    4.3753361   -2.2320941   0.14716747 
+   70000    29.735756   -1.7061457    0.9206878    3.5767878    4.3851664   -2.2516304  0.097196062 
+   71000    28.224352  -0.92217702   0.86093586    3.9507157    4.5596589   -2.2173397  0.089116669 
+   72000    29.282336    -1.056142   0.65185725    3.8735742    4.4839333   -2.4314756  0.071909704 
+   73000    26.257283  -0.64273826   0.98300685     5.063943     5.045958   -2.5544375    0.2180275 
+   74000    28.825119  -0.97736616   0.87201848      3.55875    4.3653309   -2.2303567  0.098963875 
+   75000    29.239507  -0.96508809   0.74517323    3.4306236    4.7651921   -2.6077732   0.17883654 
+   76000    27.349841  -0.50990238    1.1183613    4.4252451    4.4097775   -2.4125794   0.18483606 
+   77000    28.130197   -1.4081219   0.94921357    4.2572132    4.5162849   -2.4013797  0.073744606 
+   78000    28.235774   -0.9214321    0.6324981    3.8697686    4.8092154   -2.2272847  0.092108346 
+   79000    26.732846  -0.55949486    1.0989617    5.0088609    4.4930687    -2.277945   0.03855146 
+   80000    28.529208  -0.94244671   0.79407482     3.961106    4.3930011   -2.3127726  0.091124948 
+   81000    29.603852   -1.6116062     1.060847    3.7824932     4.151001   -1.9139868   0.19875986 
+   82000    28.232876   -1.1833011    1.0182713    3.4195758    5.1394333   -2.4632697   0.28501012 
+   83000    29.565482   -1.3479552   0.99056973    3.7851802    4.4781011   -2.7872481    0.2031991 
+   84000    28.780274   -1.3073882    1.0512637     4.004638     4.502282   -2.3789146  0.015656202 
+   85000    27.262312   -1.1305346     1.203524    4.7938623    4.1747105   -2.0952844  0.054240361 
+   86000    28.157348   -1.0662817   0.81163796    3.9912709    4.8320213    -2.255237   0.14698333 
+   87000    28.445543   -1.3365026   0.78156195    4.4767689    4.4457575   -2.5008786   0.13879386 
+   88000    27.656717   -1.1490599   0.87974869    4.4629952    4.7023033   -2.3258145  0.081904139 
+   89000    28.838821    -1.020709   0.85587929    3.7110705    4.4938307   -2.4914483   0.11447952 
+   90000    27.356497  -0.59107077   0.81879666    4.5209332    4.4703836   -2.3806717  0.071307775 
+   91000    27.780445  -0.80564513   0.94752313    3.8468943    4.2924253   -2.1011134    0.1118672 
+   92000    28.555276   -1.3514732   0.80826674    3.9590742    4.5775954   -2.4891232  0.054254978 
+   93000    28.747267   -1.2133243   0.75507246    4.1319789    4.9048611   -2.4913887   0.13045693 
+   94000    27.479343  -0.69973695   0.99696121    3.5966229     4.549025   -2.4155312   0.41745762 
+   95000    27.726945   -1.1905026    1.1120842    4.7433275    4.5386861   -2.7947142   0.33671682 
+   96000    28.021114   -1.0341645    0.6663033    4.2397505    4.6203984   -1.9904034   0.10972565 
+   97000    28.382022   -1.3916008     1.180588    4.0729621    4.6741792    -2.554927   0.13462346 
+   98000    27.895969   -0.7496449    1.3072185    4.2611888    4.3726077   -2.1320701   0.15376665 
+   99000    28.517889   -1.2183957     1.279778     3.957647    4.2638434   -2.2888407  0.042705003 
+  100000    28.109211   -1.2538948   0.83671785    4.3734766     4.544545   -2.3076497  0.042189096 
+Loop time of 2.96683 on 1 procs for 100000 steps with 34 atoms
+
+Performance: 5824.390 ns/day, 0.004 hours/ns, 33705.963 timesteps/s
+100.0% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.98759    | 0.98759    | 0.98759    |   0.0 | 33.29
+Bond    | 1.6463     | 1.6463     | 1.6463     |   0.0 | 55.49
+Neigh   | 0.007688   | 0.007688   | 0.007688   |   0.0 |  0.26
+Comm    | 0.012214   | 0.012214   | 0.012214   |   0.0 |  0.41
+Output  | 0.0010295  | 0.0010295  | 0.0010295  |   0.0 |  0.03
+Modify  | 0.25684    | 0.25684    | 0.25684    |   0.0 |  8.66
+Other   |            | 0.05519    |            |       |  1.86
+
+Nlocal:    34 ave 34 max 34 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    395 ave 395 max 395 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 395
+Ave neighs/atom = 11.6176
+Ave special neighs/atom = 9.52941
+Neighbor list builds = 237
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/examples/cmap/log.23Sep16.cmap.g++.4 b/examples/cmap/log.23Sep16.cmap.g++.4
new file mode 100644
index 0000000000..2d3efa66c6
--- /dev/null
+++ b/examples/cmap/log.23Sep16.cmap.g++.4
@@ -0,0 +1,200 @@
+LAMMPS (21 Sep 2016)
+# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016
+
+units           real
+neigh_modify    delay 2 every 1
+#newton          off
+
+boundary        p p p
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/charmm 8 12
+#pair_style      lj/charmmfsw/coul/charmmfsh 8 12
+pair_modify     mix arithmetic
+
+fix             cmap all cmap charmm22.cmap
+fix_modify      cmap energy yes
+
+read_data       gagg.data fix cmap crossterm CMAP
+  orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  34 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  12 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  33 bonds
+  reading angles ...
+  57 angles
+  reading dihedrals ...
+  75 dihedrals
+  reading impropers ...
+  7 impropers
+  4 = max # of 1-2 neighbors
+  7 = max # of 1-3 neighbors
+  13 = max # of 1-4 neighbors
+  16 = max # of special neighbors
+
+special_bonds   charmm
+fix             1 all nve
+
+#fix             1 all nvt temp 300 300 100.0
+#fix             2 all shake 1e-9 500 0 m 1.0
+
+velocity        all create 0.0 12345678 dist uniform
+
+thermo          1000
+thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp
+timestep        2.0
+
+run             100000
+Neighbor list info ...
+  1 neighbor list requests
+  update every 1 steps, delay 2 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7 -> bins = 12 12 12
+Memory usage per processor = 15.9307 Mbytes
+Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro 
+       0    26.542777  -0.93822087    1.2470497    4.8441789    4.5432816    -1.473352   0.10453023 
+    1000    28.673005  -0.47724367   0.80029132     3.151679    4.4684446   -2.3928648   0.18604953 
+    2000     27.67955    -1.170342   0.72018905    4.0400131    4.4713764   -2.5490207   0.21834436 
+    3000    29.256656  -0.35856055   0.73303546    3.7411606    4.4710568   -2.8939692   0.37728884 
+    4000    30.097549   -1.1353905   0.79007053    3.0688444    4.4091469   -2.3383587   0.20743631 
+    5000    28.357525   -1.0723742    0.9180297    3.6579424    4.8792663   -2.3185572  0.088366962 
+    6000    29.214175  -0.95299239   0.81926011    3.6805428    4.6742897   -2.9343578   0.26697816 
+    7000    27.018614  -0.52423469   0.72502751    3.8840141    4.7780958   -2.3916014   0.24952572 
+    8000    29.682494   -1.0940368   0.76113051    3.1089345    4.9357863   -2.5662256   0.14112613 
+    9000    27.853918   -0.7913741   0.79503268    4.2177256     4.146792     -2.00475  0.090585666 
+   10000     27.13754  -0.80551128    1.1325023    4.4718283    5.2460631   -3.4947725   0.11893125 
+   11000    28.277434   -1.4897448   0.90075953    4.1895717    4.3594269   -1.9553119  0.090222212 
+   12000    28.630973    -1.222206   0.67796385    3.3905661    4.9691334   -2.9052721   0.13897658 
+   13000    28.593007  -0.95684026   0.75585196    3.7242568    4.7417932   -2.3893117    0.2074121 
+   14000    26.147115   -0.6026921   0.93591488    5.1292829    4.9821952   -2.2571835   0.11872421 
+   15000     26.29432  -0.82424162     1.048979    4.5569495    5.1189308   -2.9750422   0.16195676 
+   16000    29.189992  -0.80998247   0.74093508    3.8299275    4.4536688   -2.5497538   0.19155639 
+   17000    25.878012   -0.3519646    1.0988924    4.7359591    5.3923098   -2.7211029   0.13405223 
+   18000    27.726135  -0.28229987   0.63072344    4.1777888    4.7237271   -2.2177157   0.15939372 
+   19000    27.153504  -0.66477422   0.77910129    4.2036117     5.113851   -2.3494315  0.094793307 
+   20000    28.044833   -1.2835827   0.88745367    3.9955526    4.5077788   -3.0116467   0.17197859 
+   21000    27.205696  -0.74090037    1.0023251    4.3421733     4.912671   -2.3473271   0.26089356 
+   22000    27.385785  -0.93740972   0.84554838     4.562743     4.883866   -2.2110955   0.11573301 
+   23000     27.05534  -0.95605442   0.96719024    3.9277618    5.0359014   -2.6135949   0.21368061 
+   24000    28.273378  -0.97543103    0.8983443    4.2067985    4.4782971   -2.4230505   0.30311692 
+   25000    27.477789  -0.20383849    0.8380706    3.8037992    4.8312504   -2.5831791  0.093843746 
+   26000    30.344199   -1.9773473   0.92882437    3.7821405    4.5176677   -2.3020968    0.2194307 
+   27000     27.32767   -0.9803839   0.92988865    3.7611603    5.0328211   -2.4647656   0.18213622 
+   28000     27.34208    -1.037938   0.74488346    4.1727342    4.7056812   -2.2718346   0.17741362 
+   29000    27.682777  -0.51006495   0.57074224    4.7332237    4.7080462   -2.0491512    0.2130517 
+   30000    24.925731   0.13670248   0.84976065    4.4143762    6.0677158   -3.5479173   0.28059419 
+   31000    28.623419  -0.90725708    1.0710501    3.6930688    4.6639301   -2.2225373   0.20988139 
+   32000    27.732286   -1.1948367   0.89230134    4.4398373    4.8923907   -3.5849327   0.49167488 
+   33000    28.800772   -1.5319589   0.93455495    4.1634728    4.6107706   -2.3503486   0.22636535 
+   34000    27.374398   -1.0957453   0.89450276    3.9829508     4.991786   -2.3548834   0.15869465 
+   35000     28.38753  -0.89261166   0.90000776     3.536864    4.4293294   -2.4218118   0.10640557 
+   36000    27.713974  0.088038031   0.85190574    3.8969601    4.6256355   -2.7935475   0.34671662 
+   37000     29.13007    -1.378597   0.74412556     3.131538    4.6458653   -2.9373734   0.38035616 
+   38000    28.556573   -1.4055344     1.139984    4.0035753    4.2938358    -2.489329   0.25338326 
+   39000    26.447036   -1.1829705   0.87032438    5.0804461    4.5772023   -2.7346466   0.32165802 
+   40000    27.991454  -0.64295679   0.61020872     4.165871    4.4623087   -2.2244194   0.13826991 
+   41000    29.483296   -1.2400745   0.66926627    3.3473666    4.5766617   -2.3051145   0.12171554 
+   42000    26.948627   -1.2162288    1.1440628    4.3993073    5.1176533   -2.4734485   0.15497709 
+   43000     28.04459  -0.26543193   0.83647367    3.5160747    4.6964397   -2.2805068   0.12618821 
+   44000    28.213608    -1.216128    0.9132792    4.0206483    4.9483599   -2.3387049   0.10132022 
+   45000    28.283506   -1.0390766   0.86113772     4.504509    4.7209088   -2.3043085   0.14588362 
+   46000    27.433853  -0.57912107   0.78448334    4.5998579    5.1181394   -2.6165094   0.18722528 
+   47000    27.552939   -1.1128925   0.80087638    4.3448001    4.8062869   -2.4296883    0.2702479 
+   48000    28.874034   -1.3242519   0.71770727    3.5648565    4.4671824   -2.2608958   0.16115978 
+   49000    29.216186   -1.2210307   0.76937497    3.9260628    4.7550577   -2.7316081  0.085505664 
+   50000    28.065856   -1.1545547   0.86953819    4.4137666     4.732157   -2.4450867   0.23320539 
+   51000    26.308975  -0.99728352   0.90408444    4.2400186    5.6340425   -2.2090554  0.079882158 
+   52000    28.517571   -1.5027398   0.83520278    3.8176552    4.3001251   -2.0731682    0.1665375 
+   53000     28.77579   -1.3564268   0.97253881    3.6866407    4.8532347   -2.5330776   0.17668411 
+   54000    29.135315   -1.0994106   0.67605671    3.6819254    4.3134408   -1.9796929  0.076951331 
+   55000    26.168938  -0.76247492   0.88784685    4.6533473    6.0484793   -2.1334561  0.036876985 
+   56000    27.471775  -0.68648837    1.0576168    4.0354311    4.4767052   -2.2368959   0.24950568 
+   57000    29.787083   -1.4914384    1.0702944    3.5388133    4.5173097   -2.6694464   0.27937092 
+   58000    28.705448   -1.3016617   0.63337853    3.9552713    4.4119825   -1.8774657   0.17540021 
+   59000    29.130155  -0.91647363   0.84384883    3.1076903    4.5346348   -2.3457338   0.16674486 
+   60000    26.874199  -0.81598034    1.3432151    5.1322624    4.9545484   -2.9566615   0.25950486 
+   61000    27.401306  -0.82895856    1.1636949     4.020154    4.5745928    -2.601466   0.18061051 
+   62000    28.930313   -1.5231967   0.85173243    4.3517328    4.4878662   -2.5859205    0.1755493 
+   63000     26.56874  0.026147233   0.60836216    4.4231618    4.4390677   -2.1721849   0.08594237 
+   64000    26.729023  -0.76953985   0.76734633    4.5104288    5.0886456   -2.2118551   0.11339216 
+   65000    28.900471   -1.3901477   0.86194657    4.2774976     4.498325   -2.3672362   0.20668335 
+   66000    26.884253  -0.21198879   0.98509625    4.0843117    4.4344172   -2.3289416   0.23631017 
+   67000    27.210888  -0.84075559    1.0396559    4.7253607    4.4314589   -2.2985702   0.19326507 
+   68000    28.042102   -1.1898715     1.053534    3.8748712    4.4358449   -2.3998723    0.2431659 
+   69000    28.939141   -1.6968936   0.98155912    4.0460838    5.0075204   -2.5547087   0.28645131 
+   70000     27.15577  -0.85202797    1.1469079    4.7645212    4.6133209   -2.3410451  0.086576572 
+   71000    25.507417  -0.27780727   0.95157881    4.8759406     4.853401   -2.9598705   0.41011008 
+   72000    29.804703   -1.4847015   0.96345767    3.6797304    4.3678377   -2.4594626   0.14480206 
+   73000    28.602798   -1.4906143   0.72497266    4.2442974    4.5360598   -2.3621638   0.14385651 
+   74000      28.4928  -0.91319873    1.0377472    3.8033127    4.3991601   -2.4051911  0.095567428 
+   75000     26.38168  -0.70733237    1.1557817     5.697939    4.5935618   -2.4285007  0.058980519 
+   76000     27.16626  -0.83631031   0.84844246    4.7460887    4.5801472   -2.1260014   0.12845946 
+   77000    29.040661   -1.3089499   0.80285084     4.664804    4.5215895   -2.6861939   0.13215598 
+   78000    27.477871   -1.0600977   0.88595045    4.6264017    5.4095605    -2.474411   0.10987174 
+   79000    26.151797  -0.55779685   0.91382436      4.99964    4.9184022   -2.2547241   0.22854038 
+   80000     28.14523  -0.54460026    0.8982411    3.5374555    4.3785673   -2.3196807  0.088567964 
+   81000    29.029941   -1.6467789   0.79042284    3.7269899    4.7407998   -2.3795824    0.1408727 
+   82000    27.920287  -0.72798032    1.0076975    3.4449461    4.5621371   -2.8239074   0.25103454 
+   83000    29.131054    -1.114367   0.76887285     3.459639    4.5163922    -2.607825   0.19991648 
+   84000    28.249768  -0.69944068    1.0510846    4.0436296    4.6430538   -2.4213355  0.077299966 
+   85000     28.06888  -0.62132922   0.91829312    4.1294147    4.3099557    -2.354063   0.15866186 
+   86000    28.664264   -1.1022906   0.87831695    4.5773522    4.6045802   -2.9206875   0.33950063 
+   87000    27.960967   -1.2852756   0.77694253    3.9011301    4.9114139   -3.2374868    0.3068138 
+   88000    27.190678   -1.2803268    1.1545301    4.5769709    5.2404761   -2.3825838   0.10356039 
+   89000    26.792931  -0.44516641    1.0236244    4.2007253    4.7098685   -2.3608551  0.034447062 
+   90000    27.173991  -0.87185611     1.065719    4.1953618    4.6856408   -2.6539232   0.16957757 
+   91000    28.626528    -1.239257   0.89524651    4.7048012    4.6344201   -2.7367901   0.43534143 
+   92000    27.661812    -1.109044   0.92817391    5.0294489    4.3890711   -2.4108669   0.12570139 
+   93000    28.156793   -1.0820907   0.92812693     4.938385    4.4901426   -2.4023366   0.30135781 
+   94000    28.842149   -1.3524969    1.1451109    4.3125908    4.6959035   -2.6747199    0.2254607 
+   95000    27.862247   -1.2119045    1.0218976    4.2614082    4.4931316   -2.6902934   0.16345201 
+   96000    27.084973  -0.93738328    1.3984324    4.5647189    4.4232205   -2.2834097   0.11217888 
+   97000    27.587078  -0.89397255   0.78218462    3.8944421    4.3981479   -2.4205318   0.16570942 
+   98000    27.981746   -1.2380545   0.84847869     4.311441    4.7340377   -2.4270441  0.023565612 
+   99000    27.476625   -0.8569146   0.82550381    4.1656963    4.4064921   -2.4169708     0.160814 
+  100000    26.121325  -0.63610855    1.0803389    4.9257118    4.7073263   -2.4010334  0.066303044 
+Loop time of 2.60487 on 4 procs for 100000 steps with 34 atoms
+
+Performance: 6633.735 ns/day, 0.004 hours/ns, 38389.667 timesteps/s
+99.1% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.066848   | 0.26055    | 0.6843     |  48.6 | 10.00
+Bond    | 0.067332   | 0.45486    | 0.93545    |  55.1 | 17.46
+Neigh   | 0.0078266  | 0.007863   | 0.0078835  |   0.0 |  0.30
+Comm    | 0.41829    | 1.3207     | 1.8951     |  50.8 | 50.70
+Output  | 0.0033038  | 0.0036355  | 0.0040481  |   0.4 |  0.14
+Modify  | 0.040861   | 0.15162    | 0.27091    |  27.3 |  5.82
+Other   |            | 0.4057     |            |       | 15.57
+
+Nlocal:    8.5 ave 15 max 2 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Nghost:    25.5 ave 32 max 19 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    98.75 ave 257 max 18 min
+Histogram: 1 1 1 0 0 0 0 0 0 1
+
+Total # of neighbors = 395
+Ave neighs/atom = 11.6176
+Ave special neighs/atom = 9.52941
+Neighbor list builds = 294
+Dangerous builds = 0
+Total wall time: 0:00:02
diff --git a/python/lammps.py b/python/lammps.py
index bc940c004c..0ab218bf7e 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -28,6 +28,15 @@ import os
 import select
 import re
 
+
+class MPIAbortException(Exception):
+  def __init__(self, message):
+    self.message = message
+
+  def __str__(self):
+    return repr(self.message)
+
+
 class lammps(object):
   # detect if Python is using version of mpi4py that can pass a communicator
 
@@ -43,6 +52,7 @@ class lammps(object):
   # create instance of LAMMPS
 
   def __init__(self,name="",cmdargs=None,ptr=None,comm=None):
+    self.comm = comm
 
     # determine module location
 
@@ -150,10 +160,14 @@ class lammps(object):
     if cmd: cmd = cmd.encode()
     self.lib.lammps_command(self.lmp,cmd)
 
-    if self.lib.lammps_has_error(self.lmp):
+    if self.uses_exceptions and self.lib.lammps_has_error(self.lmp):
       sb = create_string_buffer(100)
-      self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
-      raise Exception(sb.value.decode().strip())
+      error_type = self.lib.lammps_get_last_error_message(self.lmp, sb, 100)
+      error_msg = sb.value.decode().strip()
+
+      if error_type == 2:
+        raise MPIAbortException(error_msg)
+      raise Exception(error_msg)
 
   def extract_global(self,name,type):
     if name: name = name.encode()
@@ -286,6 +300,14 @@ class lammps(object):
     if name: name = name.encode()
     self.lib.lammps_scatter_atoms(self.lmp,name,type,count,data)
 
+  @property
+  def uses_exceptions(self):
+    try:
+      if self.lib.lammps_has_error:
+        return True
+    except(AttributeError):
+      return False
+
 # -------------------------------------------------------------------------
 # -------------------------------------------------------------------------
 # -------------------------------------------------------------------------
diff --git a/src/GPU/pair_eam_alloy_gpu.h b/src/GPU/pair_eam_alloy_gpu.h
index eb1ff404b0..14d9a95c30 100644
--- a/src/GPU/pair_eam_alloy_gpu.h
+++ b/src/GPU/pair_eam_alloy_gpu.h
@@ -33,6 +33,7 @@ public:
   void init_style();
   double single(int, int, int, int, double, double, double, double &);
   double memory_usage();
+  void *extract(const char *, int &) { return NULL; }
 
   int pack_forward_comm(int, int *, double *, int, int *);
   void unpack_forward_comm(int, int, double *);
diff --git a/src/GPU/pair_eam_fs_gpu.h b/src/GPU/pair_eam_fs_gpu.h
index 03c6d189b2..70edf2164e 100644
--- a/src/GPU/pair_eam_fs_gpu.h
+++ b/src/GPU/pair_eam_fs_gpu.h
@@ -33,6 +33,7 @@ public:
   void init_style();
   double single(int, int, int, int, double, double, double, double &);
   double memory_usage();
+  void *extract(const char *, int &) { return NULL; }
 
   int pack_forward_comm(int, int *, double *, int, int *);
   void unpack_forward_comm(int, int, double *);
diff --git a/src/GPU/pair_eam_gpu.h b/src/GPU/pair_eam_gpu.h
index ccc6b6f8c6..2c4731d9cf 100644
--- a/src/GPU/pair_eam_gpu.h
+++ b/src/GPU/pair_eam_gpu.h
@@ -34,6 +34,7 @@ class PairEAMGPU : public PairEAM {
   void init_style();
   double single(int, int, int, int, double, double, double, double &);
   double memory_usage();
+  void *extract(const char *, int &) { return NULL; }
 
   int pack_forward_comm(int, int *, double *, int, int *);
   void unpack_forward_comm(int, int, double *);
diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.h b/src/KOKKOS/pair_eam_alloy_kokkos.h
index 6d6f1926e5..391349d9cb 100644
--- a/src/KOKKOS/pair_eam_alloy_kokkos.h
+++ b/src/KOKKOS/pair_eam_alloy_kokkos.h
@@ -61,6 +61,7 @@ class PairEAMAlloyKokkos : public PairEAM {
   virtual ~PairEAMAlloyKokkos();
   virtual void compute(int, int);
   void init_style();
+  void *extract(const char *, int &) { return NULL; }
   void coeff(int, char **);
 
   KOKKOS_INLINE_FUNCTION
diff --git a/src/KOKKOS/pair_eam_fs_kokkos.h b/src/KOKKOS/pair_eam_fs_kokkos.h
index 6049c3eaaf..c3b0f32457 100644
--- a/src/KOKKOS/pair_eam_fs_kokkos.h
+++ b/src/KOKKOS/pair_eam_fs_kokkos.h
@@ -61,6 +61,7 @@ class PairEAMFSKokkos : public PairEAM {
   virtual ~PairEAMFSKokkos();
   virtual void compute(int, int);
   void init_style();
+  void *extract(const char *, int &) { return NULL; }
   void coeff(int, char **);
 
   KOKKOS_INLINE_FUNCTION
diff --git a/src/KOKKOS/pair_eam_kokkos.h b/src/KOKKOS/pair_eam_kokkos.h
index 89d1d61b6b..f933a4a0d7 100644
--- a/src/KOKKOS/pair_eam_kokkos.h
+++ b/src/KOKKOS/pair_eam_kokkos.h
@@ -59,6 +59,7 @@ class PairEAMKokkos : public PairEAM {
   virtual ~PairEAMKokkos();
   virtual void compute(int, int);
   void init_style();
+  void *extract(const char *, int &) { return NULL; }
 
   KOKKOS_INLINE_FUNCTION
   void operator()(TagPairEAMPackForwardComm, const int&) const;
diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp
index e2f2436a33..53fbef60e8 100644
--- a/src/MANYBODY/pair_eam.cpp
+++ b/src/MANYBODY/pair_eam.cpp
@@ -54,6 +54,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
   frho = NULL;
   rhor = NULL;
   z2r = NULL;
+  scale = NULL;
 
   frho_spline = NULL;
   rhor_spline = NULL;
@@ -232,6 +233,7 @@ void PairEAM::compute(int eflag, int vflag)
     if (eflag) {
       phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
       if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
+      phi *= scale[type[i]][type[i]];
       if (eflag_global) eng_vdwl += phi;
       if (eflag_atom) eatom[i] += phi;
     }
@@ -306,7 +308,7 @@ void PairEAM::compute(int eflag, int vflag)
           f[j][2] -= delz*fpair;
         }
 
-        if (eflag) evdwl = phi;
+        if (eflag) evdwl = scale[itype][jtype]*phi;
         if (evflag) ev_tally(i,j,nlocal,newton_pair,
                              evdwl,0.0,fpair,delx,dely,delz);
       }
diff --git a/src/MANYBODY/pair_eam.h b/src/MANYBODY/pair_eam.h
index 040497fceb..f0e9d77cee 100644
--- a/src/MANYBODY/pair_eam.h
+++ b/src/MANYBODY/pair_eam.h
@@ -54,7 +54,7 @@ class PairEAM : public Pair {
   void init_style();
   double init_one(int, int);
   double single(int, int, int, int, double, double, double, double &);
-  void *extract(const char *, int &);
+  virtual void *extract(const char *, int &);
 
   virtual int pack_forward_comm(int, int *, double *, int, int *);
   virtual void unpack_forward_comm(int, int, double *);
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
new file mode 100644
index 0000000000..39081168d8
--- /dev/null
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -0,0 +1,1432 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Implementation of the CHARMM CMAP; adds an extra energy term for the
+   peptide backbone dihedrals.  The tools/ch2lmp.pl conversion script, which
+   generates an extra section in the LAMMPS data file, is needed in order to
+   generate the info used by this fix style.
+
+   Contributing authors: 
+   Xiaohu Hu, CMB/ORNL (hux2@ornl.gov)
+   David Hyde-Volpe, Tigran Abramyan, and Robert A. Latour (Clemson University)
+   Chris Lorenz (Kings College-London)
+
+   References:
+   - MacKerell et al., J. Am. Chem. Soc. 126(2004):698-699.
+   - MacKerell et al., J. Comput. Chem. 25(2004):1400-1415.
+ -------------------------------------------------------------------------*/
+
+#include "mpi.h"
+#include "math.h"
+#include "stdlib.h"
+#include "string.h"
+#include "stdio.h"
+#include "fix_cmap.h"
+#include "atom.h"
+#include "atom_vec.h"
+#include "update.h"
+#include "respa.h"
+#include "modify.h"
+#include "domain.h"
+#include "force.h"
+#include "group.h"
+#include "comm.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+using namespace MathConst;
+
+#define MAXLINE 256
+#define LISTDELTA 10000
+#define LB_FACTOR 1.5
+
+#define CMAPMAX 6   // max # of CMAP terms stored by one atom
+#define CMAPDIM 24  // grid map dimension is 24 x 24
+#define CMAPXMIN -360.0
+#define CMAPXMIN2 -180.0
+#define CMAPDX 15.0 // 360/CMAPDIM
+
+/* ---------------------------------------------------------------------- */
+
+FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+{
+  if (narg != 4) error->all(FLERR,"Illegal fix cmap command");
+
+  restart_global = 1;
+  restart_peratom = 1;
+  peatom_flag = 1;
+  virial_flag = 1;
+  peratom_freq = 1;
+  scalar_flag = 1;
+  global_freq = 1;
+  extscalar = 1;
+  extvector = 1;
+  wd_header = 1;
+  wd_section = 1;
+
+  MPI_Comm_rank(world,&me);
+  MPI_Comm_size(world,&nprocs);
+ 
+  // allocate memory for CMAP data
+
+  memory->create(g_axis,CMAPDIM,"cmap:g_axis");
+  memory->create(cmapgrid,6,CMAPDIM,CMAPDIM,"cmap:grid");
+  memory->create(d1cmapgrid,6,CMAPDIM,CMAPDIM,"cmap:d1grid");
+  memory->create(d2cmapgrid,6,CMAPDIM,CMAPDIM,"cmap:d2grid");
+  memory->create(d12cmapgrid,6,CMAPDIM,CMAPDIM,"cmap:d12grid");
+
+  // read, initialize, broadcast cmapgrid
+
+  if (me == 0) read_grid_map(arg[3]);
+  MPI_Bcast(&cmapgrid[0][0][0],6*CMAPDIM*CMAPDIM,MPI_DOUBLE,0,world);
+
+  // perform initial allocation of atom-based arrays
+  // register with Atom class
+
+  num_crossterm = NULL;
+  crossterm_type = NULL;
+  crossterm_atom1 = NULL;
+  crossterm_atom2 = NULL;
+  crossterm_atom3 = NULL;
+  crossterm_atom4 = NULL;
+  crossterm_atom5 = NULL;
+
+  nmax_previous = 0;
+  grow_arrays(atom->nmax);
+  atom->add_callback(0);
+  atom->add_callback(1);
+
+  // local list of crossterms
+
+  ncmap = 0;
+  maxcrossterm = 0;
+  crosstermlist = NULL;
+}
+
+/* --------------------------------------------------------------------- */
+
+FixCMAP::~FixCMAP()
+{
+  // unregister callbacks to this fix from Atom class
+
+  atom->delete_callback(id,0); 
+  atom->delete_callback(id,1); 
+
+  memory->destroy(g_axis);
+  memory->destroy(cmapgrid);
+  memory->destroy(d1cmapgrid);
+  memory->destroy(d2cmapgrid);
+  memory->destroy(d12cmapgrid);
+
+  memory->destroy(crosstermlist);
+
+  memory->destroy(num_crossterm);
+  memory->destroy(crossterm_type);
+  memory->destroy(crossterm_atom1);
+  memory->destroy(crossterm_atom2);
+  memory->destroy(crossterm_atom3);
+  memory->destroy(crossterm_atom4);
+  memory->destroy(crossterm_atom5);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixCMAP::setmask()
+{
+  int mask = 0;
+  mask |= PRE_NEIGHBOR;
+  mask |= PRE_REVERSE;
+  mask |= POST_FORCE;
+  mask |= THERMO_ENERGY;
+  mask |= POST_FORCE_RESPA;
+  mask |= MIN_POST_FORCE;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::init()
+{
+  int i;
+  double angle;
+
+  i = 0;
+  angle = -180.0;
+  while (angle < 180.0) {
+    g_axis[i] = angle;
+    angle += CMAPDX;
+    i++;
+  }
+
+  // pre-compute the derivatives of the maps
+  
+  for (i = 0; i < 6; i++)
+    set_map_derivatives(cmapgrid[i],d1cmapgrid[i],d2cmapgrid[i],d12cmapgrid[i]);
+
+  // define newton_bond here in case restart file was read (not data file)
+
+  newton_bond = force->newton_bond;
+}
+
+/* --------------------------------------------------------------------- */
+
+void FixCMAP::setup(int vflag)
+{
+  pre_neighbor();
+
+  if (strstr(update->integrate_style,"verlet"))
+    post_force(vflag);
+  else {
+    ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
+    post_force_respa(vflag,nlevels_respa-1,0);
+    ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
+  }  
+}
+
+/* --------------------------------------------------------------------- */
+
+void FixCMAP::setup_pre_neighbor()
+{
+  pre_neighbor();
+}
+
+/* --------------------------------------------------------------------- */
+
+void FixCMAP::min_setup(int vflag)
+{
+  pre_neighbor();
+  post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+   store local neighbor list as if newton_bond = OFF, even if actually ON
+------------------------------------------------------------------------- */
+
+void FixCMAP::pre_neighbor()
+{
+  int i,m,itype,atom1,atom2,atom3,atom4,atom5;
+
+  // guesstimate initial length of local crossterm list
+  // if ncmap was not set (due to read_restart, no read_data),
+  //   then list will grow by LISTDELTA chunks
+
+  if (maxcrossterm == 0) {
+    if (nprocs == 1) maxcrossterm = ncmap;
+    else maxcrossterm = static_cast<int> (LB_FACTOR*ncmap/nprocs);
+    memory->create(crosstermlist,maxcrossterm,6,"cmap:crosstermlist");
+  }
+
+  int nlocal = atom->nlocal;
+
+  ncrosstermlist = 0;
+
+  for (i = 0; i < nlocal; i++) {
+    for (m = 0; m < num_crossterm[i]; m++) {
+      atom1 = atom->map(crossterm_atom1[i][m]);
+      atom2 = atom->map(crossterm_atom2[i][m]);
+      atom3 = atom->map(crossterm_atom3[i][m]);
+      atom4 = atom->map(crossterm_atom4[i][m]);
+      atom5 = atom->map(crossterm_atom5[i][m]);
+      
+      if (atom1 == -1 || atom2 == -1 || atom3 == -1 || 
+          atom4 == -1 || atom5 == -1) {
+        char str[128];
+        sprintf(str,"CMAP atoms "
+                TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " "
+                TAGINT_FORMAT " " TAGINT_FORMAT
+                " missing on proc %d at step " BIGINT_FORMAT,
+                crossterm_atom1[i][m],crossterm_atom2[i][m],
+                crossterm_atom3[i][m],crossterm_atom4[i][m],
+                crossterm_atom5[i][m],me,update->ntimestep);
+        error->one(FLERR,str);
+      }
+      atom1 = domain->closest_image(i,atom1);
+      atom2 = domain->closest_image(i,atom2);
+      atom3 = domain->closest_image(i,atom3);
+      atom4 = domain->closest_image(i,atom4);
+      atom5 = domain->closest_image(i,atom5);
+
+      if (i <= atom1 && i <= atom2 && i <= atom3 && 
+          i <= atom4 && i <= atom5) {
+        if (ncrosstermlist == maxcrossterm) {
+          maxcrossterm += LISTDELTA;
+          memory->grow(crosstermlist,maxcrossterm,6,"cmap:crosstermlist");
+        }
+        crosstermlist[ncrosstermlist][0] = atom1;
+        crosstermlist[ncrosstermlist][1] = atom2;
+        crosstermlist[ncrosstermlist][2] = atom3;
+        crosstermlist[ncrosstermlist][3] = atom4;
+        crosstermlist[ncrosstermlist][4] = atom5;
+        crosstermlist[ncrosstermlist][5] = crossterm_type[i][m];
+        ncrosstermlist++;
+      }
+    } 
+  }
+}
+
+/* ----------------------------------------------------------------------
+   store eflag, so can use it in post_force to tally per-atom energies
+------------------------------------------------------------------------- */
+
+void FixCMAP::pre_reverse(int eflag, int vflag)
+{
+  eflag_caller = eflag;
+}
+
+/* ----------------------------------------------------------------------
+   compute CMAP terms as if newton_bond = OFF, even if actually ON
+------------------------------------------------------------------------- */
+
+void FixCMAP::post_force(int vflag)
+{
+  int n,i1,i2,i3,i4,i5,type,nlist;
+  int li1, li2, mli1,mli2,mli11,mli21,t1,li3,li4,mli3,mli4,mli31,mli41;
+  int list[5];
+  // vectors needed to calculate the cross-term dihedral angles
+  double vb21x,vb21y,vb21z,vb32x,vb32y,vb32z,vb34x,vb34y,vb34z;
+  double vb23x,vb23y,vb23z;
+  double vb43x,vb43y,vb43z,vb45x,vb45y,vb45z,a1x,a1y,a1z,b1x,b1y,b1z;
+  double a2x,a2y,a2z,b2x,b2y,b2z,r32,a1sq,b1sq,a2sq,b2sq,dpr21r32,dpr34r32;
+  double dpr32r43,dpr45r43,r43,vb12x,vb12y,vb12z,vb54x,vb54y,vb54z;
+  // cross-term dihedral angles
+  double phi,psi,phi1,psi1;
+  double f1[3],f2[3],f3[3],f4[3],f5[3],vcmap[6]; 
+  double gs[4],d1gs[4],d2gs[4],d12gs[4];
+  double engfraction;
+  // vectors needed for the gradient/force calculation
+  double dphidr1x,dphidr1y,dphidr1z,dphidr2x,dphidr2y,dphidr2z;
+  double dphidr3x,dphidr3y,dphidr3z,dphidr4x,dphidr4y,dphidr4z;
+  double dpsidr1x,dpsidr1y,dpsidr1z,dpsidr2x,dpsidr2y,dpsidr2z;
+  double dpsidr3x,dpsidr3y,dpsidr3z,dpsidr4x,dpsidr4y,dpsidr4z;
+
+  // Definition of cross-term dihedrals
+
+  //         phi dihedral
+  //   |--------------------| 
+  //   a1-----a2-----a3-----a4-----a5    cross-term atoms
+  //   C      N      CA     C      N     cross-term atom types
+  //          |--------------------|
+  //               psi dihedral
+ 
+  double **x = atom->x;
+  double **f = atom->f;
+  int nlocal = atom->nlocal;
+
+  ecmap = 0.0;
+  int eflag = eflag_caller;
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = 0;
+
+  for (n = 0; n < ncrosstermlist; n++) {
+    i1 = crosstermlist[n][0];
+    i2 = crosstermlist[n][1];
+    i3 = crosstermlist[n][2];
+    i4 = crosstermlist[n][3];
+    i5 = crosstermlist[n][4];
+
+    type = crosstermlist[n][5];
+    if (type == 0) continue;
+
+    // calculate bond vectors for both dihedrals
+      
+    // phi
+    // vb21 = r2 - r1
+
+      vb21x = x[i2][0] - x[i1][0];
+      vb21y = x[i2][1] - x[i1][1];
+      vb21z = x[i2][2] - x[i1][2];
+      vb12x = -1.0*vb21x;
+      vb12y = -1.0*vb21y;
+      vb12z = -1.0*vb21z;
+      vb32x = x[i3][0] - x[i2][0];
+      vb32y = x[i3][1] - x[i2][1];
+      vb32z = x[i3][2] - x[i2][2];
+      vb23x = -1.0*vb32x;
+      vb23y = -1.0*vb32y;
+      vb23z = -1.0*vb32z;
+
+      vb34x = x[i3][0] - x[i4][0];
+      vb34y = x[i3][1] - x[i4][1];
+      vb34z = x[i3][2] - x[i4][2];
+
+      // psi
+      // bond vectors same as for phi: vb32
+
+      vb43x = -1.0*vb34x;
+      vb43y = -1.0*vb34y;
+      vb43z = -1.0*vb34z;
+    
+      vb45x = x[i4][0] - x[i5][0]; 
+      vb45y = x[i4][1] - x[i5][1]; 
+      vb45z = x[i4][2] - x[i5][2]; 
+      vb54x = -1.0*vb45x;
+      vb54y = -1.0*vb45y;
+      vb54z = -1.0*vb45z;
+ 
+      // calculate normal vectors for planes that define the dihedral angles
+      
+      a1x = vb12y*vb23z - vb12z*vb23y;
+      a1y = vb12z*vb23x - vb12x*vb23z;
+      a1z = vb12x*vb23y - vb12y*vb23x;
+      
+      b1x = vb43y*vb23z - vb43z*vb23y;
+      b1y = vb43z*vb23x - vb43x*vb23z;
+      b1z = vb43x*vb23y - vb43y*vb23x;
+      
+      a2x = vb23y*vb34z - vb23z*vb34y;
+      a2y = vb23z*vb34x - vb23x*vb34z;
+      a2z = vb23x*vb34y - vb23y*vb34x;
+      
+      b2x = vb45y*vb43z - vb45z*vb43y;
+      b2y = vb45z*vb43x - vb45x*vb43z;
+      b2z = vb45x*vb43y - vb45y*vb43x;
+      
+      // calculate terms used later in calculations
+      
+      r32 = sqrt(vb32x*vb32x + vb32y*vb32y + vb32z*vb32z);
+      a1sq = a1x*a1x + a1y*a1y + a1z*a1z;
+      b1sq = b1x*b1x + b1y*b1y + b1z*b1z;
+      
+      r43 = sqrt(vb43x*vb43x + vb43y*vb43y + vb43z*vb43z);
+      a2sq = a2x*a2x + a2y*a2y + a2z*a2z;
+      b2sq = b2x*b2x + b2y*b2y + b2z*b2z;
+      //if (a1sq<0.0001 || b1sq<0.0001 || a2sq<0.0001 || b2sq<0.0001) 
+      //  printf("a1sq b1sq a2sq b2sq: %f %f %f %f \n",a1sq,b1sq,a2sq,b2sq);
+      if (a1sq<0.0001 || b1sq<0.0001 || a2sq<0.0001 || b2sq<0.0001) continue;
+      dpr21r32 = vb21x*vb32x + vb21y*vb32y + vb21z*vb32z;
+      dpr34r32 = vb34x*vb32x + vb34y*vb32y + vb34z*vb32z;
+      dpr32r43 = vb32x*vb43x + vb32y*vb43y + vb32z*vb43z;
+      dpr45r43 = vb45x*vb43x + vb45y*vb43y + vb45z*vb43z;
+      
+      // calculate the backbone dihedral angles as VMD and GROMACS 
+
+      phi = dihedral_angle_atan2(vb21x,vb21y,vb21z,a1x,a1y,a1z,b1x,b1y,b1z,r32);
+      psi = dihedral_angle_atan2(vb32x,vb32y,vb32z,a2x,a2y,a2z,b2x,b2y,b2z,r43);
+
+      if (phi == 180.0) phi= -180.0;
+      if (psi == 180.0) psi= -180.0;
+
+      phi1 = phi;
+      if (phi1 < 0.0) phi1 += 360.0;
+      psi1 = psi;
+      if (psi1 < 0.0) psi1 += 360.0;
+
+      // find the neighbor grid point index 
+
+      li1 = int(((phi1+CMAPXMIN2)/CMAPDX)+((CMAPDIM*1.0)/2.0));
+      li2 = int(((psi1+CMAPXMIN2)/CMAPDX)+((CMAPDIM*1.0)/2.0));
+
+      li3 = int((phi-CMAPXMIN2)/CMAPDX);
+      li4 = int((psi-CMAPXMIN2)/CMAPDX);
+      mli3 = li3 % CMAPDIM;
+      mli4 = li4 % CMAPDIM;
+      mli31 = (li3+1) % CMAPDIM;
+      mli41 = (li4+1)  %CMAPDIM;
+      mli1 = li1 % CMAPDIM; 
+      mli2 = li2 % CMAPDIM;
+      mli11 = (li1+1) % CMAPDIM;
+      mli21 = (li2+1)  %CMAPDIM;
+      t1 = type-1;
+      if (t1 < 0 || t1 > 5) error->all(FLERR,"Invalid CMAP crossterm_type");
+      
+      // determine the values and derivatives for the grid square points 
+
+      gs[0] = cmapgrid[t1][mli3][mli4];
+      gs[1] = cmapgrid[t1][mli31][mli4];
+      gs[2] = cmapgrid[t1][mli31][mli41];
+      gs[3] = cmapgrid[t1][mli3][mli41];
+      d1gs[0] = d1cmapgrid[t1][mli1][mli2];  
+      d1gs[1] = d1cmapgrid[t1][mli11][mli2];
+      d1gs[2] = d1cmapgrid[t1][mli11][mli21];
+      d1gs[3] = d1cmapgrid[t1][mli1][mli21];
+      
+      d2gs[0] = d2cmapgrid[t1][mli1][mli2];  
+      d2gs[1] = d2cmapgrid[t1][mli11][mli2];
+      d2gs[2] = d2cmapgrid[t1][mli11][mli21];
+      d2gs[3] = d2cmapgrid[t1][mli1][mli21];
+      
+      d12gs[0] = d12cmapgrid[t1][mli1][mli2];  
+      d12gs[1] = d12cmapgrid[t1][mli11][mli2];
+      d12gs[2] = d12cmapgrid[t1][mli11][mli21];
+      d12gs[3] = d12cmapgrid[t1][mli1][mli21];
+      
+      // calculate the cmap energy and the gradient (dE/dphi,dE/dpsi) 
+      
+      bc_interpol(phi,psi,li3,li4,gs,d1gs,d2gs,d12gs);
+      
+      // sum up cmap energy contributions
+      
+      engfraction = 0.2 * E;
+      if (i1 < nlocal) ecmap += engfraction; 
+      if (i2 < nlocal) ecmap += engfraction; 
+      if (i3 < nlocal) ecmap += engfraction; 
+      if (i4 < nlocal) ecmap += engfraction; 
+      if (i5 < nlocal) ecmap += engfraction; 
+
+      // calculate the derivatives dphi/dr_i 
+      
+      dphidr1x = 1.0*r32/a1sq*a1x;
+      dphidr1y = 1.0*r32/a1sq*a1y;
+      dphidr1z = 1.0*r32/a1sq*a1z;
+      
+      dphidr2x = -1.0*r32/a1sq*a1x - dpr21r32/a1sq/r32*a1x + 
+        dpr34r32/b1sq/r32*b1x;
+      dphidr2y = -1.0*r32/a1sq*a1y - dpr21r32/a1sq/r32*a1y + 
+        dpr34r32/b1sq/r32*b1y;
+      dphidr2z = -1.0*r32/a1sq*a1z - dpr21r32/a1sq/r32*a1z + 
+        dpr34r32/b1sq/r32*b1z;
+
+      dphidr3x = dpr34r32/b1sq/r32*b1x - dpr21r32/a1sq/r32*a1x - r32/b1sq*b1x;
+      dphidr3y = dpr34r32/b1sq/r32*b1y - dpr21r32/a1sq/r32*a1y - r32/b1sq*b1y;
+      dphidr3z = dpr34r32/b1sq/r32*b1z - dpr21r32/a1sq/r32*a1z - r32/b1sq*b1z;
+    
+      dphidr4x = r32/b1sq*b1x;
+      dphidr4y = r32/b1sq*b1y;
+      dphidr4z = r32/b1sq*b1z;
+
+      // calculate the derivatives dpsi/dr_i 
+      
+      dpsidr1x = 1.0*r43/a2sq*a2x;
+      dpsidr1y = 1.0*r43/a2sq*a2y;
+      dpsidr1z = 1.0*r43/a2sq*a2z;
+      
+      dpsidr2x = r43/a2sq*a2x + dpr32r43/a2sq/r43*a2x - dpr45r43/b2sq/r43*b2x;
+      dpsidr2y = r43/a2sq*a2y + dpr32r43/a2sq/r43*a2y - dpr45r43/b2sq/r43*b2y;
+      dpsidr2z = r43/a2sq*a2z + dpr32r43/a2sq/r43*a2z - dpr45r43/b2sq/r43*b2z;
+      
+      dpsidr3x = dpr45r43/b2sq/r43*b2x - dpr32r43/a2sq/r43*a2x - r43/b2sq*b2x;
+      dpsidr3y = dpr45r43/b2sq/r43*b2y - dpr32r43/a2sq/r43*a2y - r43/b2sq*b2y;
+      dpsidr3z = dpr45r43/b2sq/r43*b2z - dpr32r43/a2sq/r43*a2z - r43/b2sq*b2z;
+      
+      dpsidr4x = r43/b2sq*b2x;
+      dpsidr4y = r43/b2sq*b2y;
+      dpsidr4z = r43/b2sq*b2z;
+
+      // calculate forces on cross-term atoms: F = -(dE/dPhi)*(dPhi/dr) 
+
+      f1[0] = dEdPhi*dphidr1x;
+      f1[1] = dEdPhi*dphidr1y;
+      f1[2] = dEdPhi*dphidr1z;
+      f2[0] = dEdPhi*dphidr2x + dEdPsi*dpsidr1x;
+      f2[1] = dEdPhi*dphidr2y + dEdPsi*dpsidr1y;
+      f2[2] = dEdPhi*dphidr2z + dEdPsi*dpsidr1z;
+      f3[0] = -dEdPhi*dphidr3x - dEdPsi*dpsidr2x;
+      f3[1] = -dEdPhi*dphidr3y - dEdPsi*dpsidr2y;
+      f3[2] = -dEdPhi*dphidr3z - dEdPsi*dpsidr2z;
+      f4[0] = -dEdPhi*dphidr4x - dEdPsi*dpsidr3x;
+      f4[1] = -dEdPhi*dphidr4y - dEdPsi*dpsidr3y;
+      f4[2] = -dEdPhi*dphidr4z - dEdPsi*dpsidr3z;
+      f5[0] = -dEdPsi*dpsidr4x;
+      f5[1] = -dEdPsi*dpsidr4y;
+      f5[2] = -dEdPsi*dpsidr4z;
+      
+      // apply force to each of the 5 atoms
+      
+      if (i1 < nlocal) {
+        f[i1][0] += f1[0];
+        f[i1][1] += f1[1];
+        f[i1][2] += f1[2];
+      }
+      if (i2 < nlocal) {
+        f[i2][0] += f2[0];
+        f[i2][1] += f2[1];
+        f[i2][2] += f2[2];
+      }
+      if (i3 < nlocal) {
+        f[i3][0] += f3[0];
+        f[i3][1] += f3[1];
+        f[i3][2] += f3[2];
+      }
+      if (i4 < nlocal) {
+        f[i4][0] += f4[0];
+        f[i4][1] += f4[1];
+        f[i4][2] += f4[2];
+      }
+      if (i5 < nlocal) {
+        f[i5][0] += f5[0];
+        f[i5][1] += f5[1];
+        f[i5][2] += f5[2];
+      }
+      
+      // tally energy and/or virial
+
+      if (evflag) {
+        nlist = 0;
+        if (i1 < nlocal) list[nlist++] = i1;
+        if (i2 < nlocal) list[nlist++] = i2;
+        if (i3 < nlocal) list[nlist++] = i3;
+        if (i4 < nlocal) list[nlist++] = i4;
+        if (i5 < nlocal) list[nlist++] = i5;
+        vcmap[0] = (vb12x*f1[0])+(vb32x*f3[0])+((vb43x+vb32x)*f4[0])+
+          ((vb54x+vb43x+vb32x)*f5[0]);
+        vcmap[1] = (vb12y*f1[1])+(vb32y*f3[1])+((vb43y+vb32y)*f4[1])+
+          ((vb54y+vb43y+vb32y)*f5[1]);
+        vcmap[2] = (vb12z*f1[2])+(vb32z*f3[2])+((vb43z+vb32z)*f4[2])+
+          ((vb54z+vb43z+vb32z)*f5[2]);
+        vcmap[3] = (vb12x*f1[1])+(vb32x*f3[1])+((vb43x+vb32x)*f4[1])+
+          ((vb54x+vb43x+vb32x)*f5[1]);
+        vcmap[4] = (vb12x*f1[2])+(vb32x*f3[2])+((vb43x+vb32x)*f4[2])+
+          ((vb54x+vb43x+vb32x)*f5[2]);
+        vcmap[5] = (vb12y*f1[2])+(vb32y*f3[2])+((vb43y+vb32y)*f4[2])+
+          ((vb54y+vb43y+vb32y)*f5[2]);
+        ev_tally(nlist,list,5.0,E,vcmap);
+        //ev_tally(5,list,nlocal,newton_bond,E,vcmap);
+      }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::post_force_respa(int vflag, int ilevel, int iloop)
+{
+  if (ilevel == nlevels_respa-1) post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::min_post_force(int vflag)
+{
+  post_force(vflag);
+}
+
+/* ----------------------------------------------------------------------
+   energy of CMAP term
+------------------------------------------------------------------------- */
+
+double FixCMAP::compute_scalar()
+{
+  double all;
+  MPI_Allreduce(&ecmap,&all,1,MPI_DOUBLE,MPI_SUM,world);
+  return all;
+}
+
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+// methods to read CMAP potential file, perform interpolation
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+
+void FixCMAP::read_grid_map(char *cmapfile)
+{
+  char line[MAXLINE];
+  char *chunk;
+  int i1, i2, i3, i4, i5, i6, j1, j2, j3, j4, j5, j6, counter;
+  
+  FILE *fp = fopen(cmapfile,"r");
+  if (fp == NULL) {
+    char str[128];
+    sprintf(str,"Cannot open fix cmap file %s",cmapfile);
+    error->one(FLERR,str);
+  }
+
+  for (int ix1 = 0; ix1 < 6; ix1++)
+    for (int ix2 = 0; ix2 < CMAPDIM; ix2++)
+      for (int ix3 = 0; ix3 < CMAPDIM; ix3++)
+        cmapgrid[ix1][ix2][ix3] = 0.0;
+
+  counter = 0;
+  i1 = i2 = i3 = i4 = i5 = i6 = 0;
+  j1 = j2 = j3 = j4 = j5 = j6 = 0;
+
+  while (fgets(line,MAXLINE,fp) != NULL) {
+    if (line == "" || line[0] == '#') { ;; }
+
+    // read in the cmap grid point values
+    // NOTE: The order to read the 6 grid maps is HARD-CODED, thus errors
+    //       will occur if content of the file "cmap.data" is altered
+    //
+    // Reading order of the maps:
+    // 1. Alanine map
+    // 2. Alanine before proline map
+    // 3. Proline map
+    // 4. Two adjacent prolines map
+    // 5. Glycine map
+    // 6. Glycine before proline map	
+    
+    else {
+      chunk = strtok(line, " \r\n");
+      while (chunk != NULL) {
+
+        // alanine map 
+        
+        if (counter < CMAPDIM*CMAPDIM) {
+          cmapgrid[0][i1][j1] = atof(chunk);
+          chunk = strtok(NULL, " \r\n");
+          j1++;
+          if (j1 == CMAPDIM) {
+            j1 = 0;
+            i1++;
+          }
+          counter++;
+        }
+        
+        // alanine-proline map 
+        
+        else if (counter >= CMAPDIM*CMAPDIM &&
+                 counter < 2*CMAPDIM*CMAPDIM) {
+          cmapgrid[1][i2][j2]= atof(chunk);
+          chunk = strtok(NULL, " \r\n");
+          j2++;
+          if (j2 == CMAPDIM) {
+            j2 = 0;
+            i2++;
+          }
+          counter++;
+        }
+        
+        // proline map 
+        
+        else if (counter >= 2*CMAPDIM*CMAPDIM &&
+                 counter < 3*CMAPDIM*CMAPDIM) {
+          cmapgrid[2][i3][j3] = atof(chunk);
+          chunk = strtok(NULL, " \r\n");
+          j3++;
+          if (j3 == CMAPDIM) {
+            j3 = 0;
+            i3++;
+          }
+          counter++;
+        }
+        
+        // 2 adjacent prolines map 
+        
+        else if (counter >= 3*CMAPDIM*CMAPDIM &&
+                 counter < 4*CMAPDIM*CMAPDIM) {
+          cmapgrid[3][i4][j4] = atof(chunk);
+          chunk = strtok(NULL, " \r\n");
+          j4++;
+          if (j4 == CMAPDIM) {
+            j4 = 0;
+            i4++;
+          }
+          counter++;
+        }
+        
+        // glycine map 
+        
+        else if (counter >= 4*CMAPDIM*CMAPDIM &&
+                 counter < 5*CMAPDIM*CMAPDIM) {
+          cmapgrid[4][i5][j5] = atof(chunk);
+          chunk = strtok(NULL, " \r\n");
+          j5++;
+          if (j5 == CMAPDIM) {
+            j5 = 0;
+            i5++;
+          }
+          counter++;
+        }
+        
+        // glycine-proline map 
+        
+        else if (counter >= 5*CMAPDIM*CMAPDIM &&
+                 counter < 6*CMAPDIM*CMAPDIM) {
+          cmapgrid[5][i6][j6] = atof(chunk);
+          chunk = strtok(NULL, " \r\n");
+          j6++;
+          if (j6 == CMAPDIM) {
+            j6 = 0;
+            i6++;
+          }
+          counter++;
+        }
+        
+        else break;
+      }
+    }
+  }
+  
+  fclose(fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::spline(double *y, double *ddy, int n)
+{
+  // create the 2nd dervatives of a taublated function y_i(x_i)
+  // at the tabulated points
+
+  int i, j;
+  double p, *u;
+
+  memory->create(u,n-1,"cmap:u");
+
+  ddy[0] = u[0] = 0.0;
+
+  for (i = 1; i <= n-2; i++) {
+    p = 1.0/(ddy[i-1]+4.0);
+    ddy[i] = -p;
+    u[i] = ((((6.0*y[i+1])-(12.0*y[i])+(6.0*y[i-1]))/(CMAPDX*CMAPDX))-u[i-1])*p;
+  }
+
+  ddy[n-1] = 0.0;
+
+  for (j = n-2; j >= 0; j--)
+    ddy[j] = ddy[j]*ddy[j+1] + u[j];
+
+  memory->destroy(u);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::spl_interpolate(double x, double *y, double *ddy, double &yo,
+		double &dyo)
+{
+  // perform a 1D cubic spline interpolation
+
+  int ix;
+  double a,b,a1,b1,a2,b2;
+  
+  ix = int((x-CMAPXMIN)/CMAPDX-(1./2.));
+
+  a = (CMAPXMIN+(ix*1.0)*CMAPDX-x)/CMAPDX;
+  b = (x-CMAPXMIN-(((ix-1)*1.0)*CMAPDX))/CMAPDX;
+  
+  a1 = a*a*a-a;
+  b1 = b*b*b-b;
+
+  a2 = 3.0*a*a-1.0;
+  b2 = 3.0*b*b-1.0;
+  yo = a*y[ix]+b*y[ix+1]+(a1*ddy[ix]+b1*ddy[ix+1])*(CMAPDX*CMAPDX)/6.0;
+  dyo = (y[ix+1]-y[ix])/CMAPDX-a2/6.0*CMAPDX*ddy[ix]+b2/6.0*CMAPDX*ddy[ix+1];
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::set_map_derivatives(double **map, double **d1yo, double **d2yo,
+                                   double **d12yo)
+{
+  // precompute the gradient and cross-derivatives of the map grid points.
+  // use the bicubic spline to calculate the derivatives
+
+  int i, j, k, ii, jj, xm, p;
+  double phi, psi, y, d1y, d2y, d12y, tyyk,tdyk;
+  double *tmp_y, *tmp_dy, *tmp_ddy, **tmap, **tddmap;
+  int ix;
+  double a,b,a1,b1,a2,b2;
+
+  xm = CMAPDIM/2;
+  p = CMAPDIM;
+
+  y = 0.;
+  d1y = 0.;
+  d2y = 0.;
+  d12y = 0.;
+
+  memory->create(tmp_y,CMAPDIM*2,"cmap:tmp_y");
+  memory->create(tmp_dy,CMAPDIM*2,"cmap:tmp_dy");
+  memory->create(tmp_ddy,CMAPDIM*2,"cmap:tmp_ddy");
+  memory->create(tmap,CMAPDIM*2,CMAPDIM*2,"cmap:tmap");
+  memory->create(tddmap,CMAPDIM*2,CMAPDIM*2,"cmap:tddmap");
+
+  // periodically expand the original map
+  // use the expanded map for bicubic spline interpolation, 
+  //   which is used to obtain the derivatives
+  // actual interpolation is done with bicubic interpolation
+
+  for (i = 0; i < CMAPDIM*2; i++) {
+    ii = ((i+CMAPDIM-xm)%CMAPDIM);
+    for (j = 0; j < CMAPDIM*2; j++) {
+      jj = ((j+CMAPDIM-xm)%CMAPDIM);
+      tmap[i][j] = map[ii][jj];
+    }
+  }
+  
+  for (i = 0; i < CMAPDIM*2; i++)
+    spline(tmap[i], tddmap[i], CMAPDIM*2);
+
+  for (i = xm; i < CMAPDIM+xm; i++) {
+    phi = (i-xm)*CMAPDX-180.0;
+    for (j = xm; j < CMAPDIM+xm; j++) {
+      psi = (j-xm)*CMAPDX-180.0;
+      ix = int((psi-CMAPXMIN)/CMAPDX);
+      a = (CMAPXMIN+((ix+1)*1.0)*CMAPDX-psi)/CMAPDX;
+      b = (psi-CMAPXMIN-((ix)*1.0)*CMAPDX)/CMAPDX;
+      a1 = a*a*a-a;
+      b1 = b*b*b-b;
+      a2 = 3.0*a*a-1.0;
+      b2 = 3.0*b*b-1.0;
+      for (k = 0; k < CMAPDIM*2; k++) {
+        tyyk = tmp_y[k];
+        tdyk = tmp_dy[k];
+        tyyk = a*tmap[k][ix]+b*tmap[k][ix+1]+
+          (a1*tddmap[k][ix]+b1*tddmap[k][ix+1])*(CMAPDX*CMAPDX)/6.0;
+        tdyk = (tmap[k][ix+1]-tmap[k][ix])/CMAPDX-
+          (a2/6.0*CMAPDX*tddmap[k][ix])+(b2/6.0*CMAPDX*tddmap[k][ix+1]);
+        tmp_y[k] = tyyk;
+        tmp_dy[k] = tdyk;
+      }
+      
+      spline(tmp_y,tmp_ddy,CMAPDIM+xm+xm);
+      ix = int((phi-CMAPXMIN)/CMAPDX);
+      a = (CMAPXMIN+((ix+1)*1.0)*CMAPDX-phi)/CMAPDX;
+      b = (phi-CMAPXMIN-(ix*1.0)*CMAPDX)/CMAPDX;
+      a1 = a*a*a-a;
+      b1 = b*b*b-b;
+      a2 = 3.0*a*a-1.0;
+      b2 = 3.0*b*b-1.0;
+      y = a*tmp_y[ix]+b*tmp_y[ix+1]+
+        (a1*tmp_ddy[ix]+b1*tmp_ddy[ix+1])*(CMAPDX*CMAPDX)/6.0;
+      d1y = (tmp_y[ix+1]-tmp_y[ix])/CMAPDX-
+        a2/6.0*CMAPDX*tmp_ddy[ix]+b2/6.0*CMAPDX*tmp_ddy[ix+1];
+      spline(tmp_dy,tmp_ddy,CMAPDIM+xm+xm);
+      ix = int((phi-CMAPXMIN)/CMAPDX);
+      a = (CMAPXMIN+((ix+1)*1.0)*CMAPDX-phi)/CMAPDX;
+      b = (phi-CMAPXMIN-(ix*1.0)*CMAPDX)/CMAPDX;
+      a1 = a*a*a-a;
+      b1 = b*b*b-b;
+      a2 = 3.0*a*a-1.0;
+      b2 = 3.0*b*b-1.0;
+      d2y = a*tmp_dy[ix]+b*tmp_dy[ix+1]+
+        (a1*tmp_ddy[ix]+b1*tmp_ddy[ix+1])*(CMAPDX*CMAPDX)/6.0;
+      d12y = (tmp_dy[ix+1]-tmp_dy[ix])/CMAPDX-
+        a2/6.0*CMAPDX*tmp_ddy[ix]+b2/6.0*CMAPDX*tmp_ddy[ix+1];
+      d1yo[i%p][j%p] = d1y;
+      d2yo[i%p][j%p] = d2y;
+      d12yo[i%p][j%p] = d12y;
+    }
+  }
+  
+  memory->destroy(tmp_y);
+  memory->destroy(tmp_dy);
+  memory->destroy(tmp_ddy);
+  memory->destroy(tmap);
+  memory->destroy(tddmap);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixCMAP::dihedral_angle_atan2(double fx, double fy, double fz,
+                                      double ax, double ay, double az,
+                                      double bx, double by, double bz, 
+                                      double absg)
+{
+  // calculate the dihedral angle
+
+  double angle, arg1, arg2;
+
+  arg1 = absg*(fx*bx+fy*by+fz*bz);
+  arg2 = ax*bx+ay*by+az*bz;
+
+  if (arg1 == 0 && arg2 == 0)
+    error->all(FLERR,"CMAP: atan2 function cannot take 2 zero arguments");
+  else {
+    angle = atan2(arg1,arg2);
+    angle = angle*180.0/MY_PI;
+  }
+
+  return angle;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::bc_coeff(double *gs, double *d1gs, double *d2gs, double *d12gs)
+{
+  // calculate the bicubic interpolation coefficients c_ij
+
+  static int wt[16][16] =
+    { 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+      0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
+      -3, 0, 0, 3, 0, 0, 0, 0,-2, 0, 0,-1, 0, 0, 0, 0,
+      2, 0, 0,-2, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0,
+      0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+      0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
+      0, 0, 0, 0,-3, 0, 0, 3, 0, 0, 0, 0,-2, 0, 0,-1,
+      0, 0, 0, 0, 2, 0, 0,-2, 0, 0, 0, 0, 1, 0, 0, 1,
+      -3, 3, 0, 0,-2,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+      0, 0, 0, 0, 0, 0, 0, 0,-3, 3, 0, 0,-2,-1, 0, 0,
+      9,-9, 9,-9, 6, 3,-3,-6, 6,-6,-3, 3, 4, 2, 1, 2,
+      -6, 6,-6, 6,-4,-2, 2, 4,-3, 3, 3,-3,-2,-1,-1,-2,
+      2,-2, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+      0, 0, 0, 0, 0, 0, 0, 0, 2,-2, 0, 0, 1, 1, 0, 0,
+      -6, 6,-6, 6,-3,-3, 3, 3,-4, 4, 2,-2,-2,-2,-1,-1,
+      4,-4, 4,-4, 2, 2,-2,-2, 2,-2,-2, 2, 1, 1, 1, 1 
+    };
+
+  int i, j, k, l, in;
+  double xx, x[16];
+  
+  for (i = 0; i < 4; i++) {
+    x[i] = gs[i];
+    x[i+4] = d1gs[i]*CMAPDX;
+    x[i+8] = d2gs[i]*CMAPDX;
+    x[i+12] = d12gs[i]*CMAPDX*CMAPDX;
+  }
+  
+  in = 0;
+  for (i = 0; i < 4; i++) {
+    for (j = 0; j < 4; j++) {
+      xx = 0.0;
+      for (k = 0; k < 16; k++) xx += wt[in][k]*x[k];
+      in++;
+      cij[i][j] = xx;
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixCMAP::bc_interpol(double x1, double x2, int low1, int low2, double *gs,
+                           double *d1gs, double *d2gs, double *d12gs)
+{
+  // for a given point of interest and its corresponding grid square values,
+  //   gradients and cross-derivatives
+  // calculate the interpolated value of the point of interest (POI)
+
+  int i, p=12;
+  double t, u, fac, gs1l, gs2l, gs1u, gs2u;
+
+  // set the interpolation coefficients
+
+  bc_coeff(gs,d1gs,d2gs,d12gs);
+
+  gs1l = g_axis[low1];
+  gs2l = g_axis[low2];
+
+  t = (x1-gs1l)/CMAPDX;
+  u = (x2-gs2l)/CMAPDX;
+
+  E = dEdPhi = dEdPsi = 0.0;
+
+  for (i = 3; i >= 0; i--) {
+    E = t*E + ((cij[i][3]*u+cij[i][2])*u+cij[i][1])*u+cij[i][0];
+    dEdPhi = u*dEdPhi + (3.0*cij[3][i]*t+2.0*cij[2][i])*t+cij[1][i];
+    dEdPsi = t*dEdPsi + (3.0*cij[i][3]*u+2.0*cij[i][2])*u+cij[i][1];
+  }
+  
+  dEdPhi *= (180.0/MY_PI/CMAPDX);
+  dEdPsi *= (180.0/MY_PI/CMAPDX);
+}
+
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+// methods to read and write data file
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+
+void FixCMAP::read_data_header(char *line)
+{
+  if (strstr(line,"crossterms")) {
+    sscanf(line,BIGINT_FORMAT,&ncmap);
+  } else error->all(FLERR,"Invalid read data header line for fix cmap");
+
+  // didn't set in constructor b/c this fix could be defined 
+  // before newton command
+
+  newton_bond = force->newton_bond;
+}
+
+/* ----------------------------------------------------------------------
+   unpack N lines in buf from section of data file labeled by keyword
+   id_offset is applied to atomID fields if multiple data files are read
+   store CMAP interactions as if newton_bond = OFF, even if actually ON
+------------------------------------------------------------------------- */
+
+void FixCMAP::read_data_section(char *keyword, int n, char *buf,
+                                 tagint id_offset)
+{
+  int m,tmp,itype;
+  tagint atom1,atom2,atom3,atom4,atom5;
+  char *next;
+
+  next = strchr(buf,'\n');
+  *next = '\0';
+  int nwords = atom->count_words(buf);
+  *next = '\n';
+
+  if (nwords != 7) {
+    char str[128];
+    sprintf(str,"Incorrect %s format in data file",keyword);
+    error->all(FLERR,str);
+  }
+
+  // loop over lines of CMAP crossterms
+  // tokenize the line into values
+  // add crossterm to one of my atoms, depending on newton_bond
+
+  for (int i = 0; i < n; i++) {
+    next = strchr(buf,'\n');
+    *next = '\0';
+    sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT
+           " " TAGINT_FORMAT " " TAGINT_FORMAT,
+           &tmp,&itype,&atom1,&atom2,&atom3,&atom4,&atom5);
+
+    atom1 += id_offset;
+    atom2 += id_offset;
+    atom3 += id_offset;
+    atom4 += id_offset;
+    atom5 += id_offset;
+
+    if ((m = atom->map(atom1)) >= 0) {
+      if (num_crossterm[m] == CMAPMAX)
+        error->one(FLERR,"Too many CMAP crossterms for one atom");
+      crossterm_type[m][num_crossterm[m]] = itype;
+      crossterm_atom1[m][num_crossterm[m]] = atom1;
+      crossterm_atom2[m][num_crossterm[m]] = atom2;
+      crossterm_atom3[m][num_crossterm[m]] = atom3;
+      crossterm_atom4[m][num_crossterm[m]] = atom4;
+      crossterm_atom5[m][num_crossterm[m]] = atom5;
+      num_crossterm[m]++;
+    }
+
+    if ((m = atom->map(atom2)) >= 0) {
+      if (num_crossterm[m] == CMAPMAX)
+        error->one(FLERR,"Too many CMAP crossterms for one atom");
+      crossterm_type[m][num_crossterm[m]] = itype;
+      crossterm_atom1[m][num_crossterm[m]] = atom1;
+      crossterm_atom2[m][num_crossterm[m]] = atom2;
+      crossterm_atom3[m][num_crossterm[m]] = atom3;
+      crossterm_atom4[m][num_crossterm[m]] = atom4;
+      crossterm_atom5[m][num_crossterm[m]] = atom5;
+      num_crossterm[m]++;
+    }
+
+    if ((m = atom->map(atom3)) >= 0) {
+      if (num_crossterm[m] == CMAPMAX)
+        error->one(FLERR,"Too many CMAP crossterms for one atom");
+      crossterm_type[m][num_crossterm[m]] = itype;
+      crossterm_atom1[m][num_crossterm[m]] = atom1;
+      crossterm_atom2[m][num_crossterm[m]] = atom2;
+      crossterm_atom3[m][num_crossterm[m]] = atom3;
+      crossterm_atom4[m][num_crossterm[m]] = atom4;
+      crossterm_atom5[m][num_crossterm[m]] = atom5;
+      num_crossterm[m]++;
+    }
+
+    if ((m = atom->map(atom4)) >= 0) {
+      if (num_crossterm[m] == CMAPMAX)
+        error->one(FLERR,"Too many CMAP crossterms for one atom");
+      crossterm_type[m][num_crossterm[m]] = itype;
+      crossterm_atom1[m][num_crossterm[m]] = atom1;
+      crossterm_atom2[m][num_crossterm[m]] = atom2;
+      crossterm_atom3[m][num_crossterm[m]] = atom3;
+      crossterm_atom4[m][num_crossterm[m]] = atom4;
+      crossterm_atom5[m][num_crossterm[m]] = atom5;
+      num_crossterm[m]++;
+    }
+    
+    if ((m = atom->map(atom5)) >= 0) {
+      if (num_crossterm[m] == CMAPMAX)
+        error->one(FLERR,"Too many CMAP crossterms for one atom");
+      crossterm_type[m][num_crossterm[m]] = itype;
+      crossterm_atom1[m][num_crossterm[m]] = atom1;
+      crossterm_atom2[m][num_crossterm[m]] = atom2;
+      crossterm_atom3[m][num_crossterm[m]] = atom3;
+      crossterm_atom4[m][num_crossterm[m]] = atom4;
+      crossterm_atom5[m][num_crossterm[m]] = atom5;
+      num_crossterm[m]++;
+    }
+
+    buf = next + 1;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+bigint FixCMAP::read_data_skip_lines(char *keyword)
+{
+  return ncmap;
+}
+
+/* ----------------------------------------------------------------------
+   write Mth header line to file
+   only called by proc 0
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_header(FILE *fp, int mth)
+{
+  fprintf(fp,BIGINT_FORMAT " cmap crossterms\n",ncmap);
+}
+
+/* ----------------------------------------------------------------------
+   return size I own for Mth data section
+   # of data sections = 1 for this fix
+   nx = # of crossterms owned by my local atoms
+     if newton_bond off, atom only owns crossterm if it is atom3
+   ny = columns = type + 5 atom IDs
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_section_size(int mth, int &nx, int &ny)
+{
+  int i,m;
+
+  tagint *tag = atom->tag;
+  int nlocal = atom->nlocal;
+
+  nx = 0;
+  for (i = 0; i < nlocal; i++)
+    for (m = 0; m < num_crossterm[i]; m++)
+      if (crossterm_atom3[i][m] == tag[i]) nx++;
+
+  ny = 6;
+}
+
+/* ----------------------------------------------------------------------
+   pack values for Mth data section into 2d buf
+   buf allocated by caller as owned crossterms by 6
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_section_pack(int mth, double **buf)
+{
+  int i,m;
+
+  // 1st column = CMAP type
+  // 2nd-6th columns = 5 atom IDs
+
+  tagint *tag = atom->tag;
+  int nlocal = atom->nlocal;
+
+  int n = 0;
+  for (i = 0; i < nlocal; i++) {
+    for (m = 0; m < num_crossterm[i]; m++) {
+      if (crossterm_atom3[i][m] != tag[i]) continue;
+      buf[n][0] = ubuf(crossterm_type[i][m]).d;
+      buf[n][1] = ubuf(crossterm_atom1[i][m]).d;
+      buf[n][2] = ubuf(crossterm_atom2[i][m]).d;
+      buf[n][3] = ubuf(crossterm_atom3[i][m]).d;
+      buf[n][4] = ubuf(crossterm_atom4[i][m]).d;
+      buf[n][5] = ubuf(crossterm_atom5[i][m]).d;
+      n++;
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   write section keyword for Mth data section to file
+   use Molecules or Charges if that is only field, else use fix ID
+   only called by proc 0
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_section_keyword(int mth, FILE *fp)
+{
+  fprintf(fp,"\nCMAP\n\n");
+}
+
+/* ----------------------------------------------------------------------
+   write N lines from buf to file
+   convert buf fields to int or double depending on styles
+   index can be used to prepend global numbering
+   only called by proc 0
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_data_section(int mth, FILE *fp,
+                                  int n, double **buf, int index)
+{
+  for (int i = 0; i < n; i++)
+    fprintf(fp,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT 
+            " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT "\n",
+            index+i,(int) ubuf(buf[i][0]).i,(tagint) ubuf(buf[i][1]).i,
+            (tagint) ubuf(buf[i][2]).i,(tagint) ubuf(buf[i][3]).i,
+            (tagint) ubuf(buf[i][4]).i,(tagint) ubuf(buf[i][5]).i);
+}
+
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+// methods for restart and communication
+// ----------------------------------------------------------------------
+// ----------------------------------------------------------------------
+
+/* ----------------------------------------------------------------------
+   pack entire state of Fix into one write
+------------------------------------------------------------------------- */
+
+void FixCMAP::write_restart(FILE *fp)
+{
+  if (comm->me == 0) {
+    int size = sizeof(bigint);
+    fwrite(&size,sizeof(int),1,fp);
+    fwrite(&ncmap,sizeof(bigint),1,fp);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   use state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixCMAP::restart(char *buf)
+{
+  ncmap = *((bigint *) buf);
+}
+
+/* ---------------------------------------------------------------------- 
+   pack values in local atom-based arrays for restart file 
+------------------------------------------------------------------------- */
+
+int FixCMAP::pack_restart(int i, double *buf)
+{
+  int n = 1;
+  for (int m = 0; m < num_crossterm[i]; m++) {
+    buf[n++] = ubuf(MAX(crossterm_type[i][m],-crossterm_type[i][m])).d;
+    buf[n++] = ubuf(crossterm_atom1[i][m]).d;
+    buf[n++] = ubuf(crossterm_atom2[i][m]).d;
+    buf[n++] = ubuf(crossterm_atom3[i][m]).d;
+    buf[n++] = ubuf(crossterm_atom4[i][m]).d;
+    buf[n++] = ubuf(crossterm_atom5[i][m]).d;
+  }  
+  buf[0] = n;
+
+  return n; 
+}
+
+/* ---------------------------------------------------------------------- 
+   unpack values from atom->extra array to restart the fix 
+------------------------------------------------------------------------- */
+
+void FixCMAP::unpack_restart(int nlocal, int nth)
+{
+  double **extra = atom->extra;
+
+  // skip to Nth set of extra values
+   
+   int n = 0;
+   for (int i = 0; i < nth; i++) n += static_cast<int> (extra[nlocal][n]); 
+
+   int count = static_cast<int> (extra[nlocal][n++]);
+   num_crossterm[nlocal] = (count-1)/6;
+
+   for (int m = 0; m < num_crossterm[nlocal]; m++) {
+     crossterm_type[nlocal][m] = (int) ubuf(extra[nlocal][n++]).i;
+     crossterm_atom1[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+     crossterm_atom2[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+     crossterm_atom3[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+     crossterm_atom4[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+     crossterm_atom5[nlocal][m] = (tagint) ubuf(extra[nlocal][n++]).i;
+   }
+}
+
+/* ---------------------------------------------------------------------- 
+   maxsize of any atom's restart data 
+------------------------------------------------------------------------- */
+
+int FixCMAP::maxsize_restart()
+{
+  return 1 + CMAPMAX*6; 
+}
+
+/* ---------------------------------------------------------------------- 
+   size of atom nlocal's restart data 
+------------------------------------------------------------------------- */
+
+int FixCMAP::size_restart(int nlocal)
+{
+  return 1 + num_crossterm[nlocal]*6;
+}
+
+/* ----------------------------------------------------------------------
+   allocate atom-based array
+------------------------------------------------------------------------- */
+
+void FixCMAP::grow_arrays(int nmax)
+{ 
+  num_crossterm = memory->grow(num_crossterm,nmax,"cmap:num_crossterm");
+  crossterm_type = memory->grow(crossterm_type,nmax,CMAPMAX,
+                                "cmap:crossterm_type");
+  crossterm_atom1 = memory->grow(crossterm_atom1,nmax,CMAPMAX,
+                                 "cmap:crossterm_atom1");
+  crossterm_atom2 = memory->grow(crossterm_atom2,nmax,CMAPMAX,
+                                 "cmap:crossterm_atom2");
+  crossterm_atom3 = memory->grow(crossterm_atom3,nmax,CMAPMAX,
+                                 "cmap:crossterm_atom3");
+  crossterm_atom4 = memory->grow(crossterm_atom4,nmax,CMAPMAX,
+                                 "cmap:crossterm_atom4");
+  crossterm_atom5 = memory->grow(crossterm_atom5,nmax,CMAPMAX,
+                                 "cmap:crossterm_atom5");
+
+  // must initialize num_crossterm to 0 for added atoms
+  // may never be set for some atoms when data file is read
+
+  for (int i = nmax_previous; i < nmax; i++) num_crossterm[i] = 0;
+  nmax_previous = nmax;
+}
+
+/* ----------------------------------------------------------------------
+   copy values within local atom-based array
+------------------------------------------------------------------------- */
+
+void FixCMAP::copy_arrays(int i, int j, int delflag)
+{
+  num_crossterm[j] = num_crossterm[i];
+
+  for (int k = 0; k < num_crossterm[j]; k++){
+    crossterm_type[j][k] = crossterm_type[i][k];
+    crossterm_atom1[j][k] = crossterm_atom1[i][k];
+    crossterm_atom2[j][k] = crossterm_atom2[i][k];
+    crossterm_atom3[j][k] = crossterm_atom3[i][k];
+    crossterm_atom4[j][k] = crossterm_atom4[i][k];
+    crossterm_atom5[j][k] = crossterm_atom5[i][k];
+  }
+}
+
+/* ----------------------------------------------------------------------
+   initialize one atom's array values, called when atom is created
+------------------------------------------------------------------------- */
+
+void FixCMAP::set_arrays(int i)
+{
+  num_crossterm[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+   pack values in local atom-based array for exchange with another proc
+------------------------------------------------------------------------- */
+  
+int FixCMAP::pack_exchange(int i, double *buf)
+{
+  int n = 0;
+  buf[n++] = ubuf(num_crossterm[i]).d;
+  for (int m = 0; m < num_crossterm[i]; m++) {
+    buf[n++] = ubuf(crossterm_type[i][m]).d;
+    buf[n++] = ubuf(crossterm_atom1[i][m]).d;
+    buf[n++] = ubuf(crossterm_atom2[i][m]).d;
+    buf[n++] = ubuf(crossterm_atom3[i][m]).d;
+    buf[n++] = ubuf(crossterm_atom4[i][m]).d;
+    buf[n++] = ubuf(crossterm_atom5[i][m]).d;
+  }
+  return n;
+}
+
+/* ----------------------------------------------------------------------
+   unpack values in local atom-based array from exchange with another proc
+------------------------------------------------------------------------- */
+
+int FixCMAP::unpack_exchange(int nlocal, double *buf)
+{
+  int n = 0;
+  num_crossterm[nlocal] = (int) ubuf(buf[n++]).i;
+  for (int m = 0; m < num_crossterm[nlocal]; m++) {
+    crossterm_type[nlocal][m] = (int) ubuf(buf[n++]).i;
+    crossterm_atom1[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+    crossterm_atom2[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+    crossterm_atom3[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+    crossterm_atom4[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+    crossterm_atom5[nlocal][m] = (tagint) ubuf(buf[n++]).i;
+  }
+  return n;
+}
+
+/* ----------------------------------------------------------------------
+   memory usage of local atom-based arrays
+------------------------------------------------------------------------- */
+
+double FixCMAP::memory_usage()
+{
+  int nmax = atom->nmax;
+  double bytes = nmax * sizeof(int);        // num_crossterm
+  bytes += nmax*CMAPMAX * sizeof(int);      // crossterm_type
+  bytes += 5*nmax*CMAPMAX * sizeof(int);    // crossterm_atom 12345
+  bytes += maxcrossterm*6 * sizeof(int);    // crosstermlist
+  return bytes;
+}
diff --git a/src/MOLECULE/fix_cmap.h b/src/MOLECULE/fix_cmap.h
new file mode 100644
index 0000000000..213d881e23
--- /dev/null
+++ b/src/MOLECULE/fix_cmap.h
@@ -0,0 +1,129 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(cmap,FixCMAP)
+
+#else
+
+#ifndef LMP_FIX_CMAP_H
+#define LMP_FIX_CMAP_H
+
+#include "fix.h"
+namespace LAMMPS_NS {
+
+class FixCMAP : public Fix {
+ public:
+  FixCMAP(class LAMMPS *, int, char **);
+  ~FixCMAP();
+  int setmask();
+  void init();
+  void setup(int);
+  void setup_pre_neighbor();
+  void min_setup(int);
+  void pre_neighbor();
+  void pre_reverse(int, int);
+  void post_force(int);
+  void post_force_respa(int, int, int);
+  void min_post_force(int);
+  double compute_scalar();
+
+  void read_data_header(char *);
+  void read_data_section(char *, int, char *, tagint);
+  bigint read_data_skip_lines(char *);
+  void write_data_header(FILE *, int);
+  void write_data_section_size(int, int &, int &);
+  void write_data_section_pack(int, double **);
+  void write_data_section_keyword(int, FILE *);
+  void write_data_section(int, FILE *, int, double **, int);
+
+  void write_restart(FILE *);
+  void restart(char *);
+  int pack_restart(int, double *);
+  void unpack_restart(int, int);
+  int size_restart(int);
+  int maxsize_restart();
+
+  void grow_arrays(int);
+  void copy_arrays(int, int, int);
+  void set_arrays(int);
+  int pack_exchange(int, double *);
+  int unpack_exchange(int, double *);
+
+  double memory_usage();
+ 
+ private:
+  int nprocs,me;
+  int newton_bond,eflag_caller;
+  int ctype,nlevels_respa;
+  int ncrosstermtypes,crossterm_per_atom,maxcrossterm;
+  int ncrosstermlist;
+  bigint ncmap;
+
+  int **crosstermlist;
+
+  int nmax_previous;
+  int *num_crossterm;
+  int **crossterm_type;
+  tagint **crossterm_atom1,**crossterm_atom2,**crossterm_atom3;
+  tagint **crossterm_atom4,**crossterm_atom5;
+
+  double E,dEdPhi,dEdPsi;
+  double ecmap;
+  double fcmap[4],cij[4][4];
+  double *g_axis;
+
+  // CMAP grid points obtained from external file
+
+  double ***cmapgrid;
+
+  // partial derivatives and cross-derivatives of the grid data
+
+  double ***d1cmapgrid,***d2cmapgrid,***d12cmapgrid;
+
+  // read map grid data
+
+  void read_grid_map(char *);
+
+  // read in CMAP cross terms from LAMMPS data file
+
+  void read_cmap_data(int, char *);
+
+  // pre-compute the partial and cross-derivatives of map grid points
+
+  void set_map_derivatives(double **, double **, double **, double **);
+
+  // cubic spline interpolation functions for derivatives of map grid points
+
+  void spline(double *, double *, int);
+  void spl_interpolate(double, double *, double *, double &, double &);
+
+  // calculate dihedral angles
+     
+  double dihedral_angle_atan2(double, double, double, double, double, double,
+                              double, double, double, double);
+
+  // calculate bicubic interpolation coefficient matrix c_ij
+
+  void bc_coeff(double *, double *, double *, double *);
+
+  // perform bicubic interpolation at point of interest
+
+  void bc_interpol(double, double, int, int, double *, double *, double *,
+                   double *);
+};
+}
+
+#endif
+#endif
diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp
index 66b2e7283c..e970f90ae8 100644
--- a/src/OPT/pair_eam_opt.cpp
+++ b/src/OPT/pair_eam_opt.cpp
@@ -247,6 +247,7 @@ void PairEAMOpt::eval()
     if (EFLAG) {
       double phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
       if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
+      phi *= scale[type[i]][type[i]];
       if (eflag_global) eng_vdwl += phi;
       if (eflag_atom) eatom[i] += phi;
     }
@@ -273,6 +274,7 @@ void PairEAMOpt::eval()
     double tmpfz = 0.0;
 
     fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr];
+    double* _noalias scale_i = scale[itype1+1]+1;
 
     for (jj = 0; jj < jnum; jj++) {
       j = jlist[jj];
@@ -316,12 +318,13 @@ void PairEAMOpt::eval()
         // psip needs both fp[i] and fp[j] terms since r_ij appears in two
         //   terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
         //   hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
+        // scale factor can be applied by thermodynamic integration
 
         double recip = 1.0/r;
         double phi = z2*recip;
         double phip = z2p*recip - phi*recip;
         double psip = fp[i]*rhojp + fp[j]*rhoip + phip;
-        double fpair = -psip*recip;
+        double fpair = -scale_i[jtype]*psip*recip;
 
         tmpfx += delx*fpair;
         tmpfy += dely*fpair;
@@ -332,7 +335,7 @@ void PairEAMOpt::eval()
           ff[j].z -= delz*fpair;
         }
 
-        if (EFLAG) evdwl = phi;
+        if (EFLAG) evdwl = scale_i[jtype]*phi;
 
         if (EVFLAG) ev_tally(i,j,nlocal,NEWTON_PAIR,
                              evdwl,0.0,fpair,delx,dely,delz);
diff --git a/src/Purge.list b/src/Purge.list
index 37d137e838..995385dfd4 100644
--- a/src/Purge.list
+++ b/src/Purge.list
@@ -13,6 +13,9 @@ style_kspace.h
 style_minimize.h
 style_pair.h
 style_region.h
+# deleted on 20 Sep 2016
+fix_ti_rs.cpp
+fix_ti_rs.h
 # deleted on 31 May 2016
 fix_ave_spatial_sphere.cpp
 fix_ave_spatial_sphere.h
diff --git a/src/USER-MISC/fix_ti_spring.cpp b/src/USER-MISC/fix_ti_spring.cpp
index 5f3e9d9cdf..6b9e3d63b5 100644
--- a/src/USER-MISC/fix_ti_spring.cpp
+++ b/src/USER-MISC/fix_ti_spring.cpp
@@ -12,14 +12,14 @@
 ------------------------------------------------------------------------- */
 
 /* -------------------------------------------------------------------------
-    Contributing authors: 
+    Contributing authors:
              Rodrigo Freitas (UC Berkeley) - rodrigof@berkeley.edu
              Mark Asta (UC Berkeley) - mdasta@berkeley.edu
              Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
 ------------------------------------------------------------------------- */
 
-#include "stdlib.h"
-#include "string.h"
+#include <stdlib.h>
+#include <string.h>
 #include "fix_ti_spring.h"
 #include "atom.h"
 #include "update.h"
@@ -27,12 +27,13 @@
 #include "respa.h"
 #include "memory.h"
 #include "error.h"
+#include "citeme.h"
 #include "force.h"
 
-using namespace LAMMPS_NS; 
-using namespace FixConst;  
+using namespace LAMMPS_NS;
+using namespace FixConst;
 
-static const char cite_ti_spring[] =
+static const char cite_fix_ti_spring[] =
   "ti/spring command:\n\n"
   "@article{freitas2016,\n"
   "  author={Freitas, Rodrigo and Asta, Mark and de Koning, Maurice},\n"
@@ -46,9 +47,11 @@ static const char cite_ti_spring[] =
 
 /* ---------------------------------------------------------------------- */
 
-FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) : 
-  Fix(lmp, narg, arg) 
+FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
 {
+  if (lmp->citeme) lmp->citeme->add(cite_fix_ti_spring);
+
   if (narg < 6 || narg > 8)
     error->all(FLERR,"Illegal fix ti/spring command");
 
@@ -62,22 +65,25 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
   extscalar = 1;
   extvector = 1;
 
+  // disallow resetting the time step, while this fix is defined
+  time_depend = 1;
+
   // Spring constant.
   k = force->numeric(FLERR,arg[3]);
   if (k <= 0.0) error->all(FLERR,"Illegal fix ti/spring command");
 
-  // Perform initial allocation of atom-based array.
-  // Registar with Atom class.
+  // Perform initial allocation of atom-based array
+  // Register with Atom class
   xoriginal = NULL;
   grow_arrays(atom->nmax);
   atom->add_callback(0);
   atom->add_callback(1);
 
-  // xoriginal = initial unwrapped positions of atom.
+  // xoriginal = initial unwrapped positions of atoms
 
   double **x = atom->x;
   int *mask = atom->mask;
-  tagint *image = atom->image;
+  imageint *image = atom->image;
   int nlocal = atom->nlocal;
 
   for (int i = 0; i < nlocal; i++) {
@@ -86,22 +92,22 @@ FixTISpring::FixTISpring(LAMMPS *lmp, int narg, char **arg) :
   }
 
   // Time variables.
-  t_switch = atoi(arg[4]); // Switching time.
-  t_equil = atoi(arg[5]);  // Equilibration time.
-  t0 = update->ntimestep;  // Initial time.
-  if (t_switch < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
-  if (t_equil  < 0.0) error->all(FLERR,"Illegal fix ti/spring command");
+  t0 = update->ntimestep;  // timestep of original/starting coordinates
+  t_switch = force->bnumeric(FLERR,arg[4]); // Number of steps for switching
+  t_equil  = force->bnumeric(FLERR,arg[5]); // Number of steps for equilibration
+  if ((t_switch <= 0) || (t_equil < 0))
+    error->all(FLERR,"Illegal fix ti/spring command");
 
-  // Coupling parameter initialization.
+  // Coupling parameter initialization
   sf = 1;
   if (narg > 6) {
-    if (strcmp(arg[6], "function") == 0) sf = atoi(arg[7]);
+    if (strcmp(arg[6], "function") == 0) sf = force->inumeric(FLERR,arg[7]);
     else error->all(FLERR,"Illegal fix ti/spring switching function");
-    if ((sf!=1) && (sf!=2)) 
+    if ((sf!=1) && (sf!=2))
       error->all(FLERR,"Illegal fix ti/spring switching function");
   }
-  lambda  =  switch_func(0); 
-  dlambda = dswitch_func(0); 
+  lambda  =  switch_func(0);
+  dlambda = dswitch_func(0);
 
   espring = 0.0;
 }
@@ -163,14 +169,13 @@ void FixTISpring::min_setup(int vflag)
 
 void FixTISpring::post_force(int vflag)
 {
-  // If on the first equilibration do not calculate forces.
-  int t = update->ntimestep - t0;
-  if(t < t_equil) return;
+  // do not calculate forces during equilibration
+  if ((update->ntimestep - t0) < t_equil) return;
 
   double **x = atom->x;
   double **f = atom->f;
   int *mask = atom->mask;
-  tagint *image = atom->image;
+  imageint *image = atom->image;
   int nlocal = atom->nlocal;
 
   double dx, dy, dz;
@@ -209,21 +214,24 @@ void FixTISpring::min_post_force(int vflag)
 
 /* ---------------------------------------------------------------------- */
 
-void FixTISpring::initial_integrate(int vflag) 
-{ 
-  // Update the coupling parameter value.
-  double t = update->ntimestep - (t0+t_equil); 
+void FixTISpring::initial_integrate(int vflag)
+{
+  // Update the coupling parameter value if needed
+  if ((update->ntimestep - t0) < t_equil) return;
 
-  if( (t >= 0) && (t <= t_switch) ) {
-    lambda  =  switch_func(t/t_switch); 
-    dlambda = dswitch_func(t/t_switch); 
+  const bigint t = update->ntimestep - (t0+t_equil);
+  const double r_switch = 1.0/t_switch;
+
+  if ( (t >= 0) && (t <= t_switch) ) {
+    lambda  =  switch_func(t*r_switch);
+    dlambda = dswitch_func(t*r_switch);
   }
 
-  if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
-    lambda  =    switch_func(1.0 - (t - t_switch - t_equil)/t_switch ); 
-    dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)/t_switch ); 
+  if ( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
+    lambda  =    switch_func(1.0 - (t - t_switch - t_equil)*r_switch);
+    dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch);
   }
-} 
+}
 
 /* ----------------------------------------------------------------------
    energy of stretched springs
@@ -323,11 +331,11 @@ void FixTISpring::unpack_restart(int nlocal, int nth)
   double **extra = atom->extra;
 
   // skip to Nth set of extra values
-  
+
   int m = 0;
   for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
   m++;
-  
+
   xoriginal[nlocal][0] = extra[nlocal][m++];
   xoriginal[nlocal][1] = extra[nlocal][m++];
   xoriginal[nlocal][2] = extra[nlocal][m++];
@@ -352,10 +360,10 @@ int FixTISpring::size_restart(int nlocal)
 }
 
 /* ----------------------------------------------------------------------
-     Switching function.
+     Switching function
 ------------------------------------------------------------------------- */
 
-double FixTISpring::switch_func(double t) 
+double FixTISpring::switch_func(double t)
 {
   if (sf == 1) return t;
 
@@ -365,10 +373,10 @@ double FixTISpring::switch_func(double t)
 }
 
 /* ----------------------------------------------------------------------
-     Switching function derivative.
+     Switching function derivative
 ------------------------------------------------------------------------- */
 
-double FixTISpring::dswitch_func(double t) 
+double FixTISpring::dswitch_func(double t)
 {
   if(sf == 1) return 1.0/t_switch;
 
diff --git a/src/USER-MISC/fix_ti_spring.h b/src/USER-MISC/fix_ti_spring.h
index 9b956e7076..57c0d3299a 100644
--- a/src/USER-MISC/fix_ti_spring.h
+++ b/src/USER-MISC/fix_ti_spring.h
@@ -66,9 +66,9 @@ class FixTISpring : public Fix {
   double lambda;      // Coupling parameter.
   double dlambda;     // Lambda variation with t.
   double linfo[2];    // Current lambda status.
-  int    t_switch;    // Total switching steps.
-  int    t_equil;     // Equilibration time.
-  int    t0;          // Initial time.
+  bigint t_switch;    // Total switching steps.
+  bigint t_equil;     // Equilibration time.
+  bigint t0;          // Initial time.
   int    sf;          // Switching function option.
   int    nlevels_respa;
 };
diff --git a/src/USER-MISC/pair_cdeam.h b/src/USER-MISC/pair_cdeam.h
index 1ae81af93e..934b7601a4 100644
--- a/src/USER-MISC/pair_cdeam.h
+++ b/src/USER-MISC/pair_cdeam.h
@@ -49,6 +49,8 @@ public:
   /// Reports the memory usage of this pair style to LAMMPS.
   double memory_usage();
 
+  void *extract(const char *, int &) { return NULL; }
+
   /// Parses the coefficients of the h polynomial from the end of the EAM file.
   void read_h_coeff(char* filename);
 
diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp
index 6b4ac4363e..9c28477af0 100644
--- a/src/USER-OMP/pair_eam_omp.cpp
+++ b/src/USER-OMP/pair_eam_omp.cpp
@@ -203,7 +203,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
     if (EFLAG) {
       phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
       if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
-      e_tally_thr(this, i, i, nlocal, NEWTON_PAIR, phi, 0.0, thr);
+      e_tally_thr(this, i, i, nlocal, NEWTON_PAIR, scale[type[i]][type[i]]*phi, 0.0, thr);
     }
   }
 
@@ -230,6 +230,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
     ztmp = x[i].z;
     itype = type[i];
     fxtmp = fytmp = fztmp = 0.0;
+    const double * _noalias const scale_i = scale[itype];
 
     jlist = firstneigh[i];
     jnum = numneigh[i];
@@ -274,7 +275,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
         phi = z2*recip;
         phip = z2p*recip - phi*recip;
         psip = fp[i]*rhojp + fp[j]*rhoip + phip;
-        fpair = -psip*recip;
+        fpair = -scale_i[jtype]*psip*recip;
 
         fxtmp += delx*fpair;
         fytmp += dely*fpair;
@@ -285,7 +286,7 @@ void PairEAMOMP::eval(int iifrom, int iito, ThrData * const thr)
           f[j].z -= delz*fpair;
         }
 
-        if (EFLAG) evdwl = phi;
+        if (EFLAG) evdwl = scale_i[jtype]*phi;
         if (EVFLAG) ev_tally_thr(this, i,j,nlocal,NEWTON_PAIR,
                                  evdwl,0.0,fpair,delx,dely,delz,thr);
       }
diff --git a/src/error.cpp b/src/error.cpp
index 614b62d5f0..5c24d94832 100644
--- a/src/error.cpp
+++ b/src/error.cpp
@@ -22,7 +22,12 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-Error::Error(LAMMPS *lmp) : Pointers(lmp), last_error_message(NULL) {}
+Error::Error(LAMMPS *lmp) : Pointers(lmp) {
+#ifdef LAMMPS_EXCEPTIONS
+  last_error_message = NULL;
+  last_error_type = ERROR_NONE;
+#endif
+}
 
 /* ----------------------------------------------------------------------
    called by all procs in universe
@@ -198,6 +203,7 @@ void Error::done(int status)
   exit(status);
 }
 
+#ifdef LAMMPS_EXCEPTIONS
 /* ----------------------------------------------------------------------
    return the last error message reported by LAMMPS (only used if
    compiled with -DLAMMPS_EXCEPTIONS)
@@ -208,13 +214,22 @@ char * Error::get_last_error() const
   return last_error_message;
 }
 
-
 /* ----------------------------------------------------------------------
-   set the last error message (only used if compiled with
-   -DLAMMPS_EXCEPTIONS)
+   return the type of the last error reported by LAMMPS (only used if
+   compiled with -DLAMMPS_EXCEPTIONS)
 ------------------------------------------------------------------------- */
 
-void Error::set_last_error(const char * msg)
+ErrorType Error::get_last_error_type() const
+{
+  return last_error_type;
+}
+
+/* ----------------------------------------------------------------------
+   set the last error message and error type
+   (only used if compiled with -DLAMMPS_EXCEPTIONS)
+------------------------------------------------------------------------- */
+
+void Error::set_last_error(const char * msg, ErrorType type)
 {
   delete [] last_error_message;
 
@@ -224,4 +239,6 @@ void Error::set_last_error(const char * msg)
   } else {
     last_error_message = NULL;
   }
+  last_error_type = type;
 }
+#endif
diff --git a/src/error.h b/src/error.h
index 0ca9440572..b66fe4a13b 100644
--- a/src/error.h
+++ b/src/error.h
@@ -15,41 +15,14 @@
 #define LMP_ERROR_H
 
 #include "pointers.h"
-#include <string>
-#include <exception>
+
+#ifdef LAMMPS_EXCEPTIONS
+#include "exceptions.h"
+#endif
 
 namespace LAMMPS_NS {
 
-class LAMMPSException : public std::exception
-{
-public:
-  std::string message;
-
-  LAMMPSException(std::string msg) : message(msg) {
-  }
-
-  ~LAMMPSException() throw() {
-  }
-
-  virtual const char * what() const throw() {
-    return message.c_str();
-  }
-};
-
-class LAMMPSAbortException : public LAMMPSException {
-public:
-  MPI_Comm universe;
-
-  LAMMPSAbortException(std::string msg, MPI_Comm universe) :
-    LAMMPSException(msg),
-    universe(universe)
-  {
-  }
-};
-
 class Error : protected Pointers {
-  char * last_error_message;
-
  public:
   Error(class LAMMPS *);
 
@@ -63,8 +36,15 @@ class Error : protected Pointers {
   void message(const char *, int, const char *, int = 1);
   void done(int = 0); // 1 would be fully backwards compatible
 
-  char * get_last_error() const;
-  void   set_last_error(const char * msg);
+#ifdef LAMMPS_EXCEPTIONS
+  char *    get_last_error() const;
+  ErrorType get_last_error_type() const;
+  void   set_last_error(const char * msg, ErrorType type = ERROR_NORMAL);
+
+ private:
+  char * last_error_message;
+  ErrorType last_error_type;
+#endif
 };
 
 }
diff --git a/src/exceptions.h b/src/exceptions.h
new file mode 100644
index 0000000000..121991afc5
--- /dev/null
+++ b/src/exceptions.h
@@ -0,0 +1,58 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_EXCEPTIONS_H
+#define LMP_EXCEPTIONS_H
+
+#include <mpi.h>
+#include <string>
+#include <exception>
+
+namespace LAMMPS_NS {
+
+class LAMMPSException : public std::exception
+{
+public:
+  std::string message;
+
+  LAMMPSException(std::string msg) : message(msg) {
+  }
+
+  ~LAMMPSException() throw() {
+  }
+
+  virtual const char * what() const throw() {
+    return message.c_str();
+  }
+};
+
+class LAMMPSAbortException : public LAMMPSException {
+public:
+  MPI_Comm universe;
+
+  LAMMPSAbortException(std::string msg, MPI_Comm universe) :
+    LAMMPSException(msg),
+    universe(universe)
+  {
+  }
+};
+
+enum ErrorType {
+   ERROR_NONE   = 0,
+   ERROR_NORMAL = 1,
+   ERROR_ABORT  = 2
+};
+
+}
+
+#endif
diff --git a/src/fix.cpp b/src/fix.cpp
index aa18e04762..5fd7764baa 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -139,7 +139,7 @@ void Fix::modify_params(int narg, char **arg)
     } else if (strcmp(arg[iarg],"respa") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix_modify command");
       if (!respa_level_support) error->all(FLERR,"Illegal fix_modify command");
-      int lvl = force->inumeric(FLERR,arg[1]);
+      int lvl = force->inumeric(FLERR,arg[iarg+1]);
       if (lvl < 0) error->all(FLERR,"Illegal fix_modify command");
       respa_level = lvl-1;
       iarg += 2;
diff --git a/src/fix_adapt.cpp b/src/fix_adapt.cpp
index d8deaddd28..2a3f7db1f1 100644
--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@@ -321,7 +321,7 @@ void FixAdapt::init()
         delete[] psuffix;
       }
       if (ad->pair == NULL) ad->pair = force->pair_match(pstyle,1,nsub);
-      if (ad->pair == NULL) 
+      if (ad->pair == NULL)
         error->all(FLERR,"Fix adapt pair style does not exist");
 
       void *ptr = ad->pair->extract(ad->pparam,ad->pdim);
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index 3c07977382..d3c4b12e3d 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -48,8 +48,10 @@ enum{EQUAL,ATOM};
 
 FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), vxvarstr(NULL), vyvarstr(NULL), vzvarstr(NULL),
-  xoriginal(NULL), toriginal(NULL), qoriginal(NULL), displace(NULL), velocity(NULL)
+  xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), vxvarstr(NULL), 
+  vyvarstr(NULL), vzvarstr(NULL),
+  xoriginal(NULL), toriginal(NULL), qoriginal(NULL), 
+  displace(NULL), velocity(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal fix move command");
 
diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp
index e2ce97db43..01ba81e554 100644
--- a/src/fix_nh.cpp
+++ b/src/fix_nh.cpp
@@ -54,7 +54,8 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
 tstat_flag(0), pstat_flag(0),
 rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL),
 tcomputeflag(0), pcomputeflag(0), eta(NULL), eta_dot(NULL), eta_dotdot(NULL),
-eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL), etap_mass(NULL), mpchain(0)
+eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL), 
+etap_mass(NULL), mpchain(0)
 {
   if (narg < 4) error->all(FLERR,"Illegal fix nvt/npt/nph command");
 
diff --git a/src/fix_store.cpp b/src/fix_store.cpp
index abfceda264..19d2c72f9d 100644
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@@ -40,6 +40,7 @@ vstore(NULL), astore(NULL), rbuf(NULL)
   //   0/1 flag = not-store or store peratom values in restart file
   //   nvalues = # of peratom values, N = 1 is vector, N > 1 is array
 
+  disable = 0;
   nvalues = vecflag = 0;
   flavor = UNKNOWN; 
 
@@ -230,6 +231,8 @@ void FixStore::grow_arrays(int nmax)
 
 void FixStore::copy_arrays(int i, int j, int delflag)
 {
+  if (disable) return;
+
   if (vecflag) vstore[j] = vstore[i];
   else
     for (int m = 0; m < nvalues; m++)
@@ -242,6 +245,8 @@ void FixStore::copy_arrays(int i, int j, int delflag)
 
 int FixStore::pack_exchange(int i, double *buf)
 {
+  if (disable) return 0;
+
   if (vecflag) buf[0] = vstore[i];
   else
     for (int m = 0; m < nvalues; m++)
@@ -255,6 +260,8 @@ int FixStore::pack_exchange(int i, double *buf)
 
 int FixStore::unpack_exchange(int nlocal, double *buf)
 {
+  if (disable) return 0;
+
   if (vecflag) vstore[nlocal] = buf[0];
   else
     for (int m = 0; m < nvalues; m++)
@@ -268,6 +275,11 @@ int FixStore::unpack_exchange(int nlocal, double *buf)
 
 int FixStore::pack_restart(int i, double *buf)
 {
+  if (disable) {
+    buf[0] = 0;
+    return 1;
+  }
+
   buf[0] = nvalues+1;
   if (vecflag) buf[1] = vstore[i];
   else
@@ -282,6 +294,8 @@ int FixStore::pack_restart(int i, double *buf)
 
 void FixStore::unpack_restart(int nlocal, int nth)
 {
+  if (disable) return;
+
   double **extra = atom->extra;
 
   // skip to Nth set of extra values
@@ -302,6 +316,7 @@ void FixStore::unpack_restart(int nlocal, int nth)
 
 int FixStore::maxsize_restart()
 {
+  if (disable) return 1;
   return nvalues+1;
 }
 
@@ -311,6 +326,7 @@ int FixStore::maxsize_restart()
 
 int FixStore::size_restart(int nlocal)
 {
+  if (disable) return 1;
   return nvalues+1;
 }
 
diff --git a/src/fix_store.h b/src/fix_store.h
index 9bdfc7d308..1aad563232 100644
--- a/src/fix_store.h
+++ b/src/fix_store.h
@@ -31,6 +31,7 @@ class FixStore : public Fix {
   int nvalues;           // number of per-atom values
   double *vstore;        // vector storage for GLOBAL or PERATOM
   double **astore;       // array storage for GLOBAL or PERATOM
+  int disable;        // 1 if operations (except grow) are currently disabled
 
   FixStore(class LAMMPS *, int, char **);
   ~FixStore();
diff --git a/src/library.cpp b/src/library.cpp
index 8aa1d9978e..44e2c40782 100644
--- a/src/library.cpp
+++ b/src/library.cpp
@@ -38,6 +38,45 @@
 
 using namespace LAMMPS_NS;
 
+/* ----------------------------------------------------------------------
+   Utility macros for optional code path which captures all exceptions
+   and stores the last error message. These assume there is a variable lmp
+   which is a pointer to the current LAMMPS instance.
+
+   Usage:
+
+   BEGIN_CAPTURE
+   {
+     // code paths which might throw exception
+     ...
+   }
+   END_CAPTURE
+------------------------------------------------------------------------- */
+
+#ifdef LAMMPS_EXCEPTIONS
+#define BEGIN_CAPTURE \
+  Error * error = lmp->error; \
+  try
+
+#define END_CAPTURE \
+  catch(LAMMPSAbortException & ae) { \
+    int nprocs = 0; \
+    MPI_Comm_size(ae.universe, &nprocs ); \
+    \
+    if (nprocs > 1) { \
+      error->set_last_error(ae.message.c_str(), ERROR_ABORT); \
+    } else { \
+      error->set_last_error(ae.message.c_str(), ERROR_NORMAL); \
+    } \
+  } catch(LAMMPSException & e) { \
+    error->set_last_error(e.message.c_str(), ERROR_NORMAL); \
+  }
+#else
+#define BEGIN_CAPTURE
+#define END_CAPTURE
+#endif
+
+
 /* ----------------------------------------------------------------------
    create an instance of LAMMPS and return pointer to it
    pass in command-line args and MPI communicator to run on
@@ -45,8 +84,20 @@ using namespace LAMMPS_NS;
 
 void lammps_open(int argc, char **argv, MPI_Comm communicator, void **ptr)
 {
+#ifdef LAMMPS_EXCEPTIONS
+  try
+  {
+    LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
+    *ptr = (void *) lmp;
+  }
+  catch(LAMMPSException & e) {
+    fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
+    *ptr = (void*) NULL;
+  }
+#else
   LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
   *ptr = (void *) lmp;
+#endif
 }
 
 /* ----------------------------------------------------------------------
@@ -68,8 +119,20 @@ void lammps_open_no_mpi(int argc, char **argv, void **ptr)
 
   MPI_Comm communicator = MPI_COMM_WORLD;
 
+#ifdef LAMMPS_EXCEPTIONS
+  try
+  {
+    LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
+    *ptr = (void *) lmp;
+  }
+  catch(LAMMPSException & e) {
+    fprintf(stderr, "LAMMPS Exception: %s", e.message.c_str());
+    *ptr = (void*) NULL;
+  }
+#else
   LAMMPS *lmp = new LAMMPS(argc,argv,communicator);
   *ptr = (void *) lmp;
+#endif
 }
 
 /* ----------------------------------------------------------------------
@@ -99,7 +162,12 @@ int lammps_version(void *ptr)
 void lammps_file(void *ptr, char *str)
 {
   LAMMPS *lmp = (LAMMPS *) ptr;
-  lmp->input->file(str);
+
+  BEGIN_CAPTURE
+  {
+    lmp->input->file(str);
+  }
+  END_CAPTURE
 }
 
 /* ----------------------------------------------------------------------
@@ -108,15 +176,16 @@ void lammps_file(void *ptr, char *str)
 
 char *lammps_command(void *ptr, char *str)
 {
-  LAMMPS *  lmp = (LAMMPS *) ptr;
-  Error * error = lmp->error;
+  LAMMPS *lmp = (LAMMPS *) ptr;
+  char * result = NULL;
 
-  try {
-    return lmp->input->one(str);
-  } catch(LAMMPSException & e) {
-    error->set_last_error(e.message.c_str());
-    return NULL;
+  BEGIN_CAPTURE
+  {
+    result = lmp->input->one(str);
   }
+  END_CAPTURE
+
+  return result;
 }
 
 /* ----------------------------------------------------------------------
@@ -215,58 +284,62 @@ void *lammps_extract_compute(void *ptr, char *id, int style, int type)
 {
   LAMMPS *lmp = (LAMMPS *) ptr;
 
-  int icompute = lmp->modify->find_compute(id);
-  if (icompute < 0) return NULL;
-  Compute *compute = lmp->modify->compute[icompute];
+  BEGIN_CAPTURE
+  {
+    int icompute = lmp->modify->find_compute(id);
+    if (icompute < 0) return NULL;
+    Compute *compute = lmp->modify->compute[icompute];
 
-  if (style == 0) {
-    if (type == 0) {
-      if (!compute->scalar_flag) return NULL;
-      if (compute->invoked_scalar != lmp->update->ntimestep)
-        compute->compute_scalar();
-      return (void *) &compute->scalar;
+    if (style == 0) {
+      if (type == 0) {
+        if (!compute->scalar_flag) return NULL;
+        if (compute->invoked_scalar != lmp->update->ntimestep)
+          compute->compute_scalar();
+        return (void *) &compute->scalar;
+      }
+      if (type == 1) {
+        if (!compute->vector_flag) return NULL;
+        if (compute->invoked_vector != lmp->update->ntimestep)
+          compute->compute_vector();
+        return (void *) compute->vector;
+      }
+      if (type == 2) {
+        if (!compute->array_flag) return NULL;
+        if (compute->invoked_array != lmp->update->ntimestep)
+          compute->compute_array();
+        return (void *) compute->array;
+      }
     }
-    if (type == 1) {
-      if (!compute->vector_flag) return NULL;
-      if (compute->invoked_vector != lmp->update->ntimestep)
-        compute->compute_vector();
-      return (void *) compute->vector;
+
+    if (style == 1) {
+      if (!compute->peratom_flag) return NULL;
+      if (type == 1) {
+        if (compute->invoked_peratom != lmp->update->ntimestep)
+          compute->compute_peratom();
+        return (void *) compute->vector_atom;
+      }
+      if (type == 2) {
+        if (compute->invoked_peratom != lmp->update->ntimestep)
+          compute->compute_peratom();
+        return (void *) compute->array_atom;
+      }
     }
-    if (type == 2) {
-      if (!compute->array_flag) return NULL;
-      if (compute->invoked_array != lmp->update->ntimestep)
-        compute->compute_array();
-      return (void *) compute->array;
-    }
-  }
-
-  if (style == 1) {
-    if (!compute->peratom_flag) return NULL;
-    if (type == 1) {
-      if (compute->invoked_peratom != lmp->update->ntimestep)
-        compute->compute_peratom();
-      return (void *) compute->vector_atom;
-    }
-    if (type == 2) {
-      if (compute->invoked_peratom != lmp->update->ntimestep)
-        compute->compute_peratom();
-      return (void *) compute->array_atom;
-    }
-  }
-
-  if (style == 2) {
-    if (!compute->local_flag) return NULL;
-    if (type == 1) {
-      if (compute->invoked_local != lmp->update->ntimestep)
-        compute->compute_local();
-      return (void *) compute->vector_local;
-    }
-    if (type == 2) {
-      if (compute->invoked_local != lmp->update->ntimestep)
-        compute->compute_local();
-      return (void *) compute->array_local;
+
+    if (style == 2) {
+      if (!compute->local_flag) return NULL;
+      if (type == 1) {
+        if (compute->invoked_local != lmp->update->ntimestep)
+          compute->compute_local();
+        return (void *) compute->vector_local;
+      }
+      if (type == 2) {
+        if (compute->invoked_local != lmp->update->ntimestep)
+          compute->compute_local();
+        return (void *) compute->array_local;
+      }
     }
   }
+  END_CAPTURE
 
   return NULL;
 }
@@ -300,40 +373,44 @@ void *lammps_extract_fix(void *ptr, char *id, int style, int type,
 {
   LAMMPS *lmp = (LAMMPS *) ptr;
 
-  int ifix = lmp->modify->find_fix(id);
-  if (ifix < 0) return NULL;
-  Fix *fix = lmp->modify->fix[ifix];
+  BEGIN_CAPTURE
+  {
+    int ifix = lmp->modify->find_fix(id);
+    if (ifix < 0) return NULL;
+    Fix *fix = lmp->modify->fix[ifix];
 
-  if (style == 0) {
-    double *dptr = (double *) malloc(sizeof(double));
-    if (type == 0) {
-      if (!fix->scalar_flag) return NULL;
-      *dptr = fix->compute_scalar();
-      return (void *) dptr;
+    if (style == 0) {
+      double *dptr = (double *) malloc(sizeof(double));
+      if (type == 0) {
+        if (!fix->scalar_flag) return NULL;
+        *dptr = fix->compute_scalar();
+        return (void *) dptr;
+      }
+      if (type == 1) {
+        if (!fix->vector_flag) return NULL;
+        *dptr = fix->compute_vector(i);
+        return (void *) dptr;
+      }
+      if (type == 2) {
+        if (!fix->array_flag) return NULL;
+        *dptr = fix->compute_array(i,j);
+        return (void *) dptr;
+      }
     }
-    if (type == 1) {
-      if (!fix->vector_flag) return NULL;
-      *dptr = fix->compute_vector(i);
-      return (void *) dptr;
+
+    if (style == 1) {
+      if (!fix->peratom_flag) return NULL;
+      if (type == 1) return (void *) fix->vector_atom;
+      if (type == 2) return (void *) fix->array_atom;
     }
-    if (type == 2) {
-      if (!fix->array_flag) return NULL;
-      *dptr = fix->compute_array(i,j);
-      return (void *) dptr;
+
+    if (style == 2) {
+      if (!fix->local_flag) return NULL;
+      if (type == 1) return (void *) fix->vector_local;
+      if (type == 2) return (void *) fix->array_local;
     }
   }
-
-  if (style == 1) {
-    if (!fix->peratom_flag) return NULL;
-    if (type == 1) return (void *) fix->vector_atom;
-    if (type == 2) return (void *) fix->array_atom;
-  }
-
-  if (style == 2) {
-    if (!fix->local_flag) return NULL;
-    if (type == 1) return (void *) fix->vector_local;
-    if (type == 2) return (void *) fix->array_local;
-  }
+  END_CAPTURE
 
   return NULL;
 }
@@ -369,23 +446,27 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
 {
   LAMMPS *lmp = (LAMMPS *) ptr;
 
-  int ivar = lmp->input->variable->find(name);
-  if (ivar < 0) return NULL;
+  BEGIN_CAPTURE
+  {
+    int ivar = lmp->input->variable->find(name);
+    if (ivar < 0) return NULL;
 
-  if (lmp->input->variable->equalstyle(ivar)) {
-    double *dptr = (double *) malloc(sizeof(double));
-    *dptr = lmp->input->variable->compute_equal(ivar);
-    return (void *) dptr;
-  }
+    if (lmp->input->variable->equalstyle(ivar)) {
+      double *dptr = (double *) malloc(sizeof(double));
+      *dptr = lmp->input->variable->compute_equal(ivar);
+      return (void *) dptr;
+    }
 
-  if (lmp->input->variable->atomstyle(ivar)) {
-    int igroup = lmp->group->find(group);
-    if (igroup < 0) return NULL;
-    int nlocal = lmp->atom->nlocal;
-    double *vector = (double *) malloc(nlocal*sizeof(double));
-    lmp->input->variable->compute_atom(ivar,igroup,vector,1,0);
-    return (void *) vector;
+    if (lmp->input->variable->atomstyle(ivar)) {
+      int igroup = lmp->group->find(group);
+      if (igroup < 0) return NULL;
+      int nlocal = lmp->atom->nlocal;
+      double *vector = (double *) malloc(nlocal*sizeof(double));
+      lmp->input->variable->compute_atom(ivar,igroup,vector,1,0);
+      return (void *) vector;
+    }
   }
+  END_CAPTURE
 
   return NULL;
 }
@@ -399,7 +480,14 @@ void *lammps_extract_variable(void *ptr, char *name, char *group)
 int lammps_set_variable(void *ptr, char *name, char *str)
 {
   LAMMPS *lmp = (LAMMPS *) ptr;
-  int err = lmp->input->variable->set_string(name,str);
+  int err = -1;
+
+  BEGIN_CAPTURE
+  {
+    err = lmp->input->variable->set_string(name,str);
+  }
+  END_CAPTURE
+
   return err;
 }
 
@@ -414,9 +502,14 @@ int lammps_set_variable(void *ptr, char *name, char *str)
 double lammps_get_thermo(void *ptr, char *name)
 {
   LAMMPS *lmp = (LAMMPS *) ptr;
-  double dval;
+  double dval = 0.0;
+
+  BEGIN_CAPTURE
+  {
+    lmp->output->thermo->evaluate_keyword(name,&dval);
+  }
+  END_CAPTURE
 
-  lmp->output->thermo->evaluate_keyword(name,&dval);
   return dval;
 }
 
@@ -449,79 +542,83 @@ void lammps_gather_atoms(void *ptr, char *name,
 {
   LAMMPS *lmp = (LAMMPS *) ptr;
 
-  // error if tags are not defined or not consecutive
+  BEGIN_CAPTURE
+  {
+    // error if tags are not defined or not consecutive
 
-  int flag = 0;
-  if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
-  if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
-  if (flag) {
-    if (lmp->comm->me == 0)
-      lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
-    return;
-  }
-
-  int natoms = static_cast<int> (lmp->atom->natoms);
-
-  int i,j,offset;
-  void *vptr = lmp->atom->extract(name);
-
-  // copy = Natom length vector of per-atom values
-  // use atom ID to insert each atom's values into copy
-  // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
-
-  if (type == 0) {
-    int *vector = NULL;
-    int **array = NULL;
-    if (count == 1) vector = (int *) vptr;
-    else array = (int **) vptr;
-
-    int *copy;
-    lmp->memory->create(copy,count*natoms,"lib/gather:copy");
-    for (i = 0; i < count*natoms; i++) copy[i] = 0;
-
-    tagint *tag = lmp->atom->tag;
-    int nlocal = lmp->atom->nlocal;
-
-    if (count == 1)
-      for (i = 0; i < nlocal; i++)
-        copy[tag[i]-1] = vector[i];
-    else
-      for (i = 0; i < nlocal; i++) {
-        offset = count*(tag[i]-1);
-        for (j = 0; j < count; j++)
-          copy[offset++] = array[i][0];
-      }
-
-    MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
-    lmp->memory->destroy(copy);
-
-  } else {
-    double *vector = NULL;
-    double **array = NULL;
-    if (count == 1) vector = (double *) vptr;
-    else array = (double **) vptr;
-
-    double *copy;
-    lmp->memory->create(copy,count*natoms,"lib/gather:copy");
-    for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
-
-    tagint *tag = lmp->atom->tag;
-    int nlocal = lmp->atom->nlocal;
-
-    if (count == 1) {
-      for (i = 0; i < nlocal; i++)
-        copy[tag[i]-1] = vector[i];
-    } else {
-      for (i = 0; i < nlocal; i++) {
-        offset = count*(tag[i]-1);
-        for (j = 0; j < count; j++)
-          copy[offset++] = array[i][j];
-      }
+    int flag = 0;
+    if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
+    if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
+    if (flag) {
+      if (lmp->comm->me == 0)
+        lmp->error->warning(FLERR,"Library error in lammps_gather_atoms");
+      return;
     }
 
-    MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
-    lmp->memory->destroy(copy);
+    int natoms = static_cast<int> (lmp->atom->natoms);
+
+    int i,j,offset;
+    void *vptr = lmp->atom->extract(name);
+
+    // copy = Natom length vector of per-atom values
+    // use atom ID to insert each atom's values into copy
+    // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
+
+    if (type == 0) {
+      int *vector = NULL;
+      int **array = NULL;
+      if (count == 1) vector = (int *) vptr;
+      else array = (int **) vptr;
+
+      int *copy;
+      lmp->memory->create(copy,count*natoms,"lib/gather:copy");
+      for (i = 0; i < count*natoms; i++) copy[i] = 0;
+
+      tagint *tag = lmp->atom->tag;
+      int nlocal = lmp->atom->nlocal;
+
+      if (count == 1)
+        for (i = 0; i < nlocal; i++)
+          copy[tag[i]-1] = vector[i];
+      else
+        for (i = 0; i < nlocal; i++) {
+          offset = count*(tag[i]-1);
+          for (j = 0; j < count; j++)
+            copy[offset++] = array[i][0];
+        }
+
+      MPI_Allreduce(copy,data,count*natoms,MPI_INT,MPI_SUM,lmp->world);
+      lmp->memory->destroy(copy);
+
+    } else {
+      double *vector = NULL;
+      double **array = NULL;
+      if (count == 1) vector = (double *) vptr;
+      else array = (double **) vptr;
+
+      double *copy;
+      lmp->memory->create(copy,count*natoms,"lib/gather:copy");
+      for (i = 0; i < count*natoms; i++) copy[i] = 0.0;
+
+      tagint *tag = lmp->atom->tag;
+      int nlocal = lmp->atom->nlocal;
+
+      if (count == 1) {
+        for (i = 0; i < nlocal; i++)
+          copy[tag[i]-1] = vector[i];
+      } else {
+        for (i = 0; i < nlocal; i++) {
+          offset = count*(tag[i]-1);
+          for (j = 0; j < count; j++)
+            copy[offset++] = array[i][j];
+        }
+      }
+
+      MPI_Allreduce(copy,data,count*natoms,MPI_DOUBLE,MPI_SUM,lmp->world);
+      lmp->memory->destroy(copy);
+    }
   }
+  END_CAPTURE
 }
 
 /* ----------------------------------------------------------------------
@@ -538,69 +635,74 @@ void lammps_scatter_atoms(void *ptr, char *name,
 {
   LAMMPS *lmp = (LAMMPS *) ptr;
 
-  // error if tags are not defined or not consecutive or no atom map
+  BEGIN_CAPTURE
+  {
+    // error if tags are not defined or not consecutive or no atom map
 
-  int flag = 0;
-  if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
-  if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
-  if (lmp->atom->map_style == 0) flag = 1;
-  if (flag) {
-    if (lmp->comm->me == 0)
-      lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms");
-    return;
-  }
-
-  int natoms = static_cast<int> (lmp->atom->natoms);
-
-  int i,j,m,offset;
-  void *vptr = lmp->atom->extract(name);
-
-  // copy = Natom length vector of per-atom values
-  // use atom ID to insert each atom's values into copy
-  // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
-
-  if (type == 0) {
-    int *vector = NULL;
-    int **array = NULL;
-    if (count == 1) vector = (int *) vptr;
-    else array = (int **) vptr;
-    int *dptr = (int *) data;
-
-    if (count == 1) {
-      for (i = 0; i < natoms; i++)
-        if ((m = lmp->atom->map(i+1)) >= 0)
-          vector[m] = dptr[i];
-    } else {
-      for (i = 0; i < natoms; i++)
-        if ((m = lmp->atom->map(i+1)) >= 0) {
-          offset = count*i;
-          for (j = 0; j < count; j++)
-            array[m][j] = dptr[offset++];
-        }
+    int flag = 0;
+    if (lmp->atom->tag_enable == 0 || lmp->atom->tag_consecutive() == 0) flag = 1;
+    if (lmp->atom->natoms > MAXSMALLINT) flag = 1;
+    if (lmp->atom->map_style == 0) flag = 1;
+    if (flag) {
+      if (lmp->comm->me == 0)
+        lmp->error->warning(FLERR,"Library error in lammps_scatter_atoms");
+      return;
     }
-  } else {
-    double *vector = NULL;
-    double **array = NULL;
-    if (count == 1) vector = (double *) vptr;
-    else array = (double **) vptr;
-    double *dptr = (double *) data;
 
-    if (count == 1) {
-      for (i = 0; i < natoms; i++)
-        if ((m = lmp->atom->map(i+1)) >= 0)
-          vector[m] = dptr[i];
+    int natoms = static_cast<int> (lmp->atom->natoms);
+
+    int i,j,m,offset;
+    void *vptr = lmp->atom->extract(name);
+
+    // copy = Natom length vector of per-atom values
+    // use atom ID to insert each atom's values into copy
+    // MPI_Allreduce with MPI_SUM to merge into data, ordered by atom ID
+
+    if (type == 0) {
+      int *vector = NULL;
+      int **array = NULL;
+      if (count == 1) vector = (int *) vptr;
+      else array = (int **) vptr;
+      int *dptr = (int *) data;
+
+      if (count == 1) {
+        for (i = 0; i < natoms; i++)
+          if ((m = lmp->atom->map(i+1)) >= 0)
+            vector[m] = dptr[i];
+      } else {
+        for (i = 0; i < natoms; i++)
+          if ((m = lmp->atom->map(i+1)) >= 0) {
+            offset = count*i;
+            for (j = 0; j < count; j++)
+              array[m][j] = dptr[offset++];
+          }
+      }
     } else {
-      for (i = 0; i < natoms; i++) {
-        if ((m = lmp->atom->map(i+1)) >= 0) {
-          offset = count*i;
-          for (j = 0; j < count; j++)
-            array[m][j] = dptr[offset++];
+      double *vector = NULL;
+      double **array = NULL;
+      if (count == 1) vector = (double *) vptr;
+      else array = (double **) vptr;
+      double *dptr = (double *) data;
+
+      if (count == 1) {
+        for (i = 0; i < natoms; i++)
+          if ((m = lmp->atom->map(i+1)) >= 0)
+            vector[m] = dptr[i];
+      } else {
+        for (i = 0; i < natoms; i++) {
+          if ((m = lmp->atom->map(i+1)) >= 0) {
+            offset = count*i;
+            for (j = 0; j < count; j++)
+              array[m][j] = dptr[offset++];
+          }
         }
       }
     }
   }
+  END_CAPTURE
 }
 
+#ifdef LAMMPS_EXCEPTIONS
 /* ----------------------------------------------------------------------
    Check if a new error message
 ------------------------------------------------------------------------- */
@@ -613,6 +715,9 @@ int lammps_has_error(void *ptr) {
 
 /* ----------------------------------------------------------------------
    Copy the last error message of LAMMPS into a character buffer
+   The return value encodes which type of error it is.
+   1 = normal error (recoverable)
+   2 = abort error (non-recoverable)
 ------------------------------------------------------------------------- */
 
 int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
@@ -620,9 +725,11 @@ int lammps_get_last_error_message(void *ptr, char * buffer, int buffer_size) {
   Error * error = lmp->error;
 
   if(error->get_last_error()) {
+    int error_type = error->get_last_error_type();
     strncpy(buffer, error->get_last_error(), buffer_size-1);
-    error->set_last_error(NULL);
-    return 1;
+    error->set_last_error(NULL, ERROR_NONE);
+    return error_type;
   }
   return 0;
 }
+#endif
diff --git a/src/library.h b/src/library.h
index 5cb128fdb9..e4dffc63d1 100644
--- a/src/library.h
+++ b/src/library.h
@@ -45,8 +45,10 @@ int lammps_get_natoms(void *);
 void lammps_gather_atoms(void *, char *, int, int, void *);
 void lammps_scatter_atoms(void *, char *, int, int, void *);
 
+#ifdef LAMMPS_EXCEPTIONS
 int lammps_has_error(void *);
 int lammps_get_last_error_message(void *, char *, int);
+#endif
 
 #ifdef __cplusplus
 }
diff --git a/src/version.h b/src/version.h
index c55689c662..35c0f59e69 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "20 Sep 2016"
+#define LAMMPS_VERSION "26 Sep 2016"
diff --git a/tools/ch2lmp/README b/tools/ch2lmp/README
index eb994ccb6f..fa031bd757 100755
--- a/tools/ch2lmp/README
+++ b/tools/ch2lmp/README
@@ -11,35 +11,40 @@ In this directory, you should find:
 3) An "example" folder containing an example of how to use these tools.
 4) An "other" folder containing other potentially useful tools.
 
-In addition, you will need to provide the following input for 
+In addition, you will need to provide the following input for
 charmm2lammps.pl:
+
 1) a CHARMM parameter file (par_<forcefield>.prm)
 2) a CHARMM topology file (top_<forcefield>.rtf)
 3) a CHARMM coordinates file or pdb file (<project>.crd or <project>.pdb)
+   (NOTE: a .pdb file is required if the -cmap option is used)
 4) a CHARMM psf file (<project>.psf)
 
 To use the charmm2lammps.pl script, type: "perl charmm2lammps.pl
-[-option[=#]] <forcefield> <project>" where <forcefield> is the name
-of the CHARMM FF you are using, (i.e. all22_prot), and <project> is
-the common name of your *.crd and *.psf files. The options for the
-script are listed below. If the option requires a parameter, the
-syntax must be [-option[=#]], (i.e. -border=5).
+<forcefield> <project> [-option=value ...]" where <forcefield> is the
+name of the CHARMM FF you are using, (i.e. all22_prot), and <project>
+is the common name of your *.crd and *.psf files.  Possible options
+are listed next.  If the option requires a parameter, the syntax
+should be -option=value (e.g. -border=5).
 
--help        "display available options",                                    
--charmm      "add charmm types to LAMMPS data file",                    
--water       "add TIP3P water [default: 1 g/cc]",                       
--ions        "add (counter)ions using Na+ and Cl- [default: 0 mol/l]",  
--center      "recenter atoms",                                          
--quiet       "do not print info",                                       
--pdb_ctrl    "output project_ctrl.pdb",                                 
--l           "set x-, y-, and z-dimensions simultaneously",             
--lx          "x-dimension of simulation box",                           
--ly          "y-dimension of simulation box",                           
--lz          "z-dimension of simulation box",                           
--border      "add border to all sides of simulation box [default: 0 A]",
--ax          "rotation around x-axis",                                  
--ay          "rotation around y-axis",                                  
--az          "rotation around z-axis"                                   
+-help        display available options
+-charmm      add charmm types to LAMMPS data file
+-water       add TIP3P water [default: 1 g/cc]
+-ions        add (counter)ions using Na+ and Cl- [default: 0 mol/l]
+-center      recenter atoms
+-quiet       do not print info
+-pdb_ctrl    output project_ctrl.pdb
+-l           set x-, y-, and z-dimensions simultaneously
+-lx          x-dimension of simulation box
+-ly          y-dimension of simulation box
+-lz          z-dimension of simulation box
+-border      add border to all sides of simulation box [default: 0 A]
+-ax          rotation around x-axis
+-ay          rotation around y-axis
+-az          rotation around z-axis           
+-cd          correction for dihedral for carbohydrate systems
+-cmap        add CMAP section to data file and fix cmap command lines in 
+               input script" (NOTE: requires use of *.pdb file)
 
 In the "example" folder, you will find example files that were created
 by following the steps below. These steps describe how to take a
@@ -100,7 +105,22 @@ molecule. The -pdb_ctrl option produces the 1ac7_ctrl.pdb file that
 can be visualized in a standard visualization package such as VMD. The
 -charmm option put comments into the LAMMPS data file (everything
 after the # sign is a comment) for user convenience in tracking atom
-types etc. according to CHARMM nomenclature.
+types etc. according to CHARMM nomenclature.   
+
+The example molecule provided above (i.e., 1ac7) is a DNA fragment.
+If instead, a peptide longer than 2 amino acid residues or a protein
+is to be modeled, the '-cmap' option should be used. This will add a
+section at the end of the data file with the heading of 'CMAP' that
+will contain cmap crossterm corrections for the phi-psi dihedrals for
+the amino acid residues. You will then need to also copy the
+appropriate file for the cmap crossterms into your directory and be
+sure that you are using the appropriate cmap crossterms that go with
+the respective version of the charmm force field that is being used
+(e.g, cmap22.data or cmap36.data). This is necessary to account for
+the fact that the CHARMM group has provided updated cmap correction
+terms for use with the c36 and more recent version of the charmm
+protein force field.  Copies of cmap22.data and cmap36.data are
+provided in the tools/ch2lmp directory.
 
 The default timestep in the LAMMPS *.in file is set to 0.5 fs, which
 can typically be increased to 2 fs after equilibration if the bonds
@@ -109,9 +129,9 @@ delay on neigh_modify can probably increased to 5 or so to improve
 speed.
 
 The -ions option allows the user to neutralize the simulation cell
-with Na+ or Cl- counterions if the molecule has a net
-charge. Additional salt can be added by increasing the default
-concentration (i.e. -ions=0.5).
+with Na+ or Cl- counterions if the molecule has a net charge
+Additional salt can be added by increasing the default concentration
+(e.g. -ions=0.5).
 
 ** In the "other" file folder, you will find:
 
@@ -126,5 +146,3 @@ concentration (i.e. -ions=0.5).
 3) A 3rd party perl script called "crd2pdb.pl"
 
 4) A 3rd party fortran code called "pdb_to_crd.f"
-
-
diff --git a/tools/ch2lmp/charmm2lammps.pl b/tools/ch2lmp/charmm2lammps.pl
index 8e43a06cab..0e39f589da 100644
--- a/tools/ch2lmp/charmm2lammps.pl
+++ b/tools/ch2lmp/charmm2lammps.pl
@@ -28,22 +28,43 @@
 #    20050630	Fixed symbol issues arising from salt addition
 #    20060818	Changed reading of pdb format to read exact columns
 #    20070109	Changed AddMass() to use $max_id correctly
-#    20160114   Added compatibility for parameter files that use IMPROPERS instead of IMPROPER
-#               Print warning when not all parameters are detected. Set correct number of atom types.
-#    20160613   Fix off-by-one issue in atom type validation check
-#               Replace -charmm command line flag with -nohints flag
-#               and enable type hints in data file by default.
-#               Add hints also to section headers
-#               Add a brief minimization to example input template.
+#    20130508   Added 'CMAP crossterms' section at the end of the data file
+#    20131001   Added instructions in CMAP section to fix problem if 'ter' 
+#                 is not designated in .pdb file to identify last amino acid
 #    
 #    General	Many thanks to Paul S. Crozier for checking script validity
 #    		against his projects.
+#
+# ------------------------------------------------------------------------------
+#    NOTE: This current version was modified by Xiaohu Hu (hux2@ornl.gov)
+#    DATE: April, May 2009
+#          Then finalized to complete addition of CMAP terms to data file
+#            by Robert A. Latour, Clemson University (latourr@clemson.edu)
+#            and Chris Lorenz, King's College (chris.lorenz@kcl.ac.uk)
+#    DATE: May, 2013
+#
+#    The original code of charmm2lammps.pl is modified
+#
+#     1. to fix the double-counting problem in 1-4 interaction associated
+#        with the carbon-hydrate 6-rings containing systems. (See subroutine
+#        DihedralCorrect6Ring, activated with the option "-cd")
+#          
+#     2. to add a new section "CMAP" which is a list of the peptide 
+#        backbone dihedrals cross terms. A modifed LAMMPS version will be
+#        needed to be able to use this feature. (See subroutine CharmmCmap,
+#        activated with the option "-cmap")
+#     
+#    These subroutines are independent from the original charmm2lammps.pl, i.e.
+#    the original code of charmm2lammps.pl is unchanged. The new routines only
+#    evaluate and modify the output generated by the original charmm2lammps.pl.
+# -----------------------------------------------------------------------------
+
 
 # Initialization
 
   sub Test
   {
-    my $name		= shift(@_);
+    my $name		= shift(@_); # "@_" = argument passed to the subroutine
     
     printf("Error: file %s not found\n", $name) if (!scalar(stat($name)));
     return !scalar(stat($name));
@@ -54,11 +75,13 @@
   {
     my $k		= 0;
     my @dir		= ("x", "y", "z");
-    my @options		= ("-help", "-nohints", "-water", "-ions", "-center",
+
+    # Modified by Xiaohu Hu, May 2009. Options "-cmap" and "-cdihedral" added
+    my @options		= ("-help", "-charmm", "-water", "-ions", "-center",
 			   "-quiet", "-pdb_ctrl", "-l", "-lx", "-ly", "-lz", 
-			   "-border", "-ax", "-ay", "-az");
-    my @remarks		= ("display this message",
-                           "do not print type and style hints in data file",
+			   "-border", "-ax", "-ay", "-az", "-cd", "-cmap");
+    my @remarks		= ("display this message", 
+			   "add charmm types to LAMMPS data file",
 			   "add TIP3P water [default: 1 g/cc]",
 			   "add (counter)ions using Na+ and Cl- [default: 0 mol/l]",
 			   "recenter atoms",
@@ -71,14 +94,20 @@
 			   "add border to all sides of simulation box [default: 0 A]",
 			   "rotation around x-axis",
 			   "rotation around y-axis",
-			   "rotation around z-axis"
+			   "rotation around z-axis",
+			   "use the 6-ring dihedral correction",
+			   "generate the CMAP section"
 			 );
     my $notes;
     
     $program		= "charmm2lammps";
-    $version		= "1.8.3";
-    $year		= "2016";
-    $add		= 1;
+#    $version		= "1.8.2.5 beta"; # Modified by Xiaohu Hu, Dec 2009
+    $version		= "1.8.2.6 beta"; # Modified by Robert Latour & Chris Lorenz, May 2013
+#    $year		= "2009"; # Modified by Xiaohu Hu, April 2009
+    $year		= "2013"; # Modified by Robert Latour & Chris Lorenz, May 2013
+    $cmap		= 0; # Added by Xiaohu Hu, May 2009
+    $cdihedral		= 0; # Added by Xiaohu Hu, May 2009
+    $add		= 0;
     $water_dens		= 0;
     $ions		= 0;
     $info		= 1;
@@ -112,7 +141,7 @@
     
     foreach (@ARGV)
     {
-      if (substr($_, 0, 1) eq "-")
+      if (substr($_, 0, 1) eq "-") # if the first letter of the aguement is "-" = an option
       {
 	my $k		= 0;
         my @tmp		= split("=");
@@ -123,23 +152,24 @@
 	  last if ($tmp[0] eq substr($_, 0 , length($tmp[0])));
 	  ++$k;
 	}
-	$help		= 1 if (!$k--);                              # -help
-	$add		= 0 if (!$k--);                              # -nohints
-	$water_dens	= ($tmp[1] ne "" ? $tmp[1] : 1) if (!$k--);  # -water
-	$ion_molar	= abs($tmp[1]) if (!$k);                     # -ions
-	$ions		= 1 if (!$k--);                              # ...
-	$center		= 1 if (!$k--);                              # -center
-	$info		= 0 if (!$k--);                              # -quiet
-	$pdb_ctrl	= $switch if (!$k--);                        # -pdb_ctrl
-	my $flag	= $k--;                                      # -l
-        $L[0]		= abs($tmp[1]) if (!($flag && $k--));        # -lx
-        $L[1]		= abs($tmp[1]) if (!($flag && $k--));        # -ly
-        $L[2]		= abs($tmp[1]) if (!($flag && $k--));        # -lz
-        $border		= abs($tmp[1]) if (!$k--);                   # -border
-	@R		= M_Dot(M_Rotate(0, $tmp[1]), @R) if (!$k--);# -ax
-	@R		= M_Dot(M_Rotate(1, $tmp[1]), @R) if (!$k--);# -ay
-	@R		= M_Dot(M_Rotate(2, $tmp[1]), @R) if (!$k--);# -az
-        print("Warning: ignoring unknown command line flag: $tmp[0]\n");
+	$help		= 1 if (!$k--);
+	$add		= 1 if (!$k--);
+	$water_dens	= ($tmp[1] ne "" ? $tmp[1] : 1) if (!$k--);
+	$ion_molar	= abs($tmp[1]) if (!$k);
+	$ions		= 1 if (!$k--);
+	$center		= 1 if (!$k--);
+	$info		= 0 if (!$k--);
+	$pdb_ctrl	= $switch if (!$k--);
+	my $flag	= $k--;
+        $L[0]		= abs($tmp[1]) if (!($flag && $k--));
+        $L[1]		= abs($tmp[1]) if (!($flag && $k--));
+        $L[2]		= abs($tmp[1]) if (!($flag && $k--));
+        $border		= abs($tmp[1]) if (!$k--);
+	@R		= M_Dot(M_Rotate(0, $tmp[1]), @R) if (!$k--);
+	@R		= M_Dot(M_Rotate(1, $tmp[1]), @R) if (!$k--);
+	@R		= M_Dot(M_Rotate(2, $tmp[1]), @R) if (!$k--);
+	$cdihedral      = 1 if (!$k--); # Added by Xiaohu Hu, May 2009
+	$cmap           = 1 if (!$k--); # Added by Xiaohu Hu, May 2009
       }
       else
       {
@@ -150,7 +180,7 @@
     $water_dens		= 1 if ($ions && !$water_dens);
     if (($k<2)||$help)
     {
-      printf("\n%s v%s (c)%s by Pieter J. in \'t Veld for SNL\n\n",
+      printf("\n%s v%s (c)%s by Pieter J. in \'t Veld for SNL\nwith 6-ring dihedral correction and CMAP added by X. Hu, 2009\n\n",
         $program, $version, $year);
       printf("Usage:\n  %s.pl [-option[=#] ..] forcefield project\n\n",$program);
       printf("Options:\n");
@@ -161,7 +191,7 @@
       printf("\nNotes:\n%s\n", $notes);
       exit(-1);
     }
-    else { printf("\n%s v%s (c)%s\n\n", $program, $version, $year) if ($info); }
+    else { printf("%s v%s (c)%s\n\n", $program, $version, $year) if ($info); }
     my $flag		= Test($Parameters = "par_$forcefield.prm");
     $flag		|= Test($Topology = "top_$forcefield.rtf");
     $flag		|= Test($Pdb = "$project.pdb")
@@ -300,7 +330,7 @@
  
   sub PSFConnectivity
   {
-    my $n		= PSFGoto(bonds);
+    my $n = PSFGoto(bonds); # $n = the total number of bonds
 
     return if (scalar(@nconnect));
     printf("Info: creating connectivity\n") if ($info);
@@ -312,7 +342,6 @@
     }
   }
 
-
   sub PSFDihedrals					# hack to accomodate
   {							# LAMMPS' way of calc
     $idihedral		= 0;				# LJ 1-4 interactions
@@ -343,7 +372,6 @@
     return $ndihedral;
   }
 	    
-  
   sub CreatePSFIndex					# make an index of id
   {							# locations
     my @psf_ids		= ("!NATOM","!NBOND:","!NTHETA:","!NPHI:","!NIMPHI:");
@@ -363,26 +391,24 @@
     }
   }
 
- 
-  sub PSFGoto						# goto $ident in <PSF>
+  sub PSFGoto	# goto $ident in <PSF> and return the total number of $ident
   {
     CreatePSFIndex() if (!scalar(%PSFIndex));
     my $id		= shift(@_);
-    my @n 		= split(" ", $PSFIndex{$id});
+    my @n 		= split(" ", $PSFIndex{$id}); # = 1 if the $ident is found
     
     @PSFBuffer		= ();
     # return PSFDihedrals() if ($id eq "dihedrals");
     if (!scalar(@n))
     {
       printf("Warning: PSF index for $id not found\n");
-      seek(PSF, 0, SEEK_END);
+      seek(PSF, 0, SEEK_END); # set file-handle position to the EOF
       return -1;
     }
     seek(PSF, $n[0], SEEK_SET);
     return $n[1];
   }
 
-
   sub PSFGet
   {
     if ($dihedral_flag)
@@ -400,7 +426,7 @@
   }
 
 
-  sub PSFWrite
+      	sub PSFWrite
   {
     my $items		= shift(@_);
     my $n		= $items;
@@ -516,14 +542,11 @@
     
   sub Markers
   {
-    my %markers = (
-      NONBONDED => '0',
-      BONDS     => '1',
-      ANGLES    => '2',
-      DIHEDRALS => '3',
-      IMPROPERS => '4',
-      IMPROPER  => '4'
-    );
+    my %markers;
+    my $n		= 0;
+
+    foreach ("NONBONDED", "BONDS", "ANGLES", "DIHEDRALS", "IMPROPER") {
+      $markers{$_}	= $n++;	}
     return %markers;
   }
 
@@ -613,7 +636,7 @@
   {							# <PARAMETERS>
     my $mode		= shift(@_);			# bonded mode
     return if (($mode>3)||($mode<0));
-    
+  
     my $items		= (2, 3, 4, 4)[$mode];		# items per entry
     my $name		= ("bond", "angle", "dihedral", "improper")[$mode];
     my $read		= 0;
@@ -688,7 +711,7 @@
 
   sub SetScreeningFactor				# set screening factor
   {
-    my $id		= shift(@_);
+    my $id		= shift(@_); # @_ has the form: ($variable, float no.)
     my $value		= shift(@_);
     my $new		= "";
     
@@ -702,7 +725,6 @@
     $parms[$id]		= $new;
   }
   
-    
   sub CorrectDihedralParameters
   {
     my $n		= PSFGoto(dihedrals);
@@ -713,15 +735,20 @@
     my $first;
     my $last;
     
-    for (my $i=0; $i<$n; ++$i)
+    for (my $i=0; $i<$n; ++$i) # loop over all dihedrals
     {
-      my @bonded	= PSFGet(4);
+      my @bonded	= PSFGet(4); 
       my @tmp		= ();
       foreach (@bonded) { push(@tmp, $ids{$atom_types[$_]}); }
       $id1 		= $link{CreateID(@tmp)}-1;
       $first		= $bonded[0];
       $last		= $bonded[3];
+      
       if ($first>$last) { my $tmp = $first; $first = $last; $last = $tmp; }
+      
+      # if the condition "$id2 = $hash{$hash_id = $first." ".$last}" is false, which means
+      # the id isn't in the hash, then it will be added, otherwise means this condition is
+      # true and the 
       if (($id2 = $hash{$hash_id = $first." ".$last}) eq "") 
       {
 	$hash{$hash_id}	= $id1;				# add id to hash
@@ -1010,7 +1037,7 @@
 
   sub WriteLAMMPSHeader					# print lammps header
   {
-    printf(LAMMPS "LAMMPS data file. CGCMM style. atom_style full. Created by $program v$version on %s\n", `date`);
+    printf(LAMMPS "Created by $program v$version on %s\n", `date`);
     printf(LAMMPS "%12d  atoms\n", $natoms);
     printf(LAMMPS "%12d  bonds\n", $nbonds);
     printf(LAMMPS "%12d  angles\n", $nangles);
@@ -1114,7 +1141,7 @@
 	      {
 		my @xyz	= V_Add(@p, @p_water[$i,$i+1,$i+2]);
 		@xyz	= V_Add(@xyz, @Center) if (!$center);
-		printf(LAMMPS "%8d %7d %5d %9.6g %11.8g %11.8g %11.8g%s\n",
+		printf(LAMMPS "%8d %7d %5d %9.6g %16.12g %16.12g %16.12g%s\n",
 		  ++$k, $res, $par[$j], $charge[$j], $xyz[0], $xyz[1],
 		  $xyz[2], $add ? "  # ".$types[$par[$j]-1] : "");
 		printf(PDB_CTRL "ATOM %6.6s %-4.4s %-3.3s %5.5s %3.3s ".
@@ -1164,7 +1191,7 @@
     
     CRDGoto(atoms);
     $net_charge		= 0;
-    printf(LAMMPS "Atoms # full\n\n") if ($n>0);
+    printf(LAMMPS "Atoms\n\n") if ($n>0);
     for (my $i=0; $i<$n; ++$i)
     {
       my @crd		= $pdb ? NextPDB2CRD() : split(" ", <CRD>);
@@ -1172,7 +1199,7 @@
       my @xyz		= MV_Dot(@R, @crd[-6, -5, -4]);
       @xyz		= V_Subtr(@xyz, @Center) if ($center);
       if ($crd[-2]!=$res[1]) { ++$res[0]; $res[1] = $crd[-2]; }
-      printf(LAMMPS "%8d %7d %5d %9.6g %11.7g %11.7g %11.7g%s\n", ++$k,
+      printf(LAMMPS "%8d %7d %5d %9.6g %16.12g %16.12g %16.12g%s\n", ++$k,
        	$res[0], $link{$atom_types[$k]}, $psf[6], $xyz[0], $xyz[1], $xyz[2],
 	$add ? "  # ".$types[$link{$atom_types[$k]}-1] : "");
       printf(PDB_CTRL "ATOM %6.6s %-4.4s %-4.4s %4.4s %3.3s ".
@@ -1198,7 +1225,6 @@
   {
     my $mode		= shift(@_)+1;
     my $header		= ("Pair","Bond","Angle","Dihedral","Improper")[$mode];
-    my $hint            = ("lj/charmm/coul/long", "harmonic", "charmm", "charmm", "harmonic")[$mode];
     my $n		= (4, 2, 4, 4, 2)[$mode];
     my $k		= 0;
 
@@ -1212,7 +1238,7 @@
       @parms		= Delete(1, @parms) if ($mode==3);
     }
     return 0 if (!scalar(@parms));
-    printf(LAMMPS "%s Coeffs # %s\n\n", $header, $hint);
+    printf(LAMMPS "%s Coeffs\n\n", $header);
     for (my $i=0; $i<scalar(@parms); ++$i)
     {
       if ($parms[$i] ne "")
@@ -1222,7 +1248,7 @@
 	  my @tmp	= split(" ");
           printf(LAMMPS "%8d", ++$k);
           for (my $j=0; $j<$n; ++$j) { 
-	    printf(LAMMPS " %10.7g", $j<scalar(@tmp) ? $tmp[$j] : 0); }
+	    printf(LAMMPS " %16.12g", $j<scalar(@tmp) ? $tmp[$j] : 0); }
           printf(LAMMPS "%s\n", $add ? "  # ".$types[$i] : "");
 	}
       } else { ++$k; }
@@ -1392,11 +1418,6 @@
     CreateCorrectedPairCoefficients();
     for (my $i=0; $i<scalar(@types); ++$i) { $types[$i] = $ids{$types[$i]}; }
     $natom_types	= WriteParameters(-1);	# pairs
-    if ($#types+1 > $natom_types) {
-      print "Warning: $#types atom types present, but only $natom_types pair coeffs found\n";
-      # reset to what is found while determining the number of atom types.
-      $natom_types = $#types+1;
-    }
     $natoms		= WriteAtoms();
     $nbond_types	= WriteParameters(0);	# bonds
     $nbonds		= WriteBonded(0);
@@ -1428,15 +1449,29 @@
     printf(LAMMPS "# Created by $program v$version on %s\n", `date`);
     printf(LAMMPS "units           real\n");		# general
     printf(LAMMPS "neigh_modify    delay 2 every 1\n\n");
+
+    printf(LAMMPS "boundary        p p p\n\n");
     printf(LAMMPS "atom_style      full\n");		# styles
     printf(LAMMPS "bond_style      harmonic\n") if ($nbond_types);
     printf(LAMMPS "angle_style     charmm\n") if ($nangle_types);
     printf(LAMMPS "dihedral_style  charmm\n") if ($ndihedral_types);
     printf(LAMMPS "improper_style  harmonic\n\n") if ($nimproper_types);
-    printf(LAMMPS "pair_style      lj/charmm/coul/long 8 10\n");
+    printf(LAMMPS "# if cutoffs to be used for electrostatics, use pair_style lj/charmmfsw/coul/charmmfsh\n");
+    printf(LAMMPS "#    and delete or comment out kspace_style\n");
+    printf(LAMMPS "pair_style      lj/charmm/coul/long 8 12\n");
     printf(LAMMPS "pair_modify     mix arithmetic\n");
     printf(LAMMPS "kspace_style    pppm 1e-4\n\n");
-    printf(LAMMPS "read_data       $project.data\n\n");	# read data
+  
+    if ($cmap) {
+      printf(LAMMPS "# Modify following lines to provide directory path cmap.data and 'project'.data files\n");
+      printf(LAMMPS "fix             cmap all cmap /directoryPath/.../cmap36.data\n");
+      printf(LAMMPS "fix_modify      cmap energy yes\n");
+      printf(LAMMPS "read_data       /directoryPath/.../$project.data fix cmap crossterm CMAP\n\n");
+    }else{
+      printf(LAMMPS "# Modify following line to provide directory path for 'project'.data file\n");
+      printf(LAMMPS "read_data       /directoryPath/.../$project.data\n\n");	# read data
+    }
+
     if ($coefficients ne "")				# corrected coeffs
     {
       foreach (split(":", $coefficients))
@@ -1446,16 +1481,15 @@
       printf(LAMMPS "\n");
     }
     printf(LAMMPS "special_bonds   charmm\n");		# invoke charmm
-    printf(LAMMPS "thermo          1\n");		# set thermo style
-    printf(LAMMPS "thermo_style    multi\n");
-    printf(LAMMPS "timestep        0.5\n\n");		# 0.5 ps time step
-    printf(LAMMPS "minimize 0.0 0.0 1000 10000\n\n");   # take off the edge
     printf(LAMMPS "fix             1 all nve\n");
     printf(LAMMPS "fix             2 all shake 1e-6 500 0 m 1.0\n")
       if ($shake eq "");				# shake all H-bonds
     printf(LAMMPS "fix             2 all shake 1e-6 500 0 m 1.0 a %s\n",$shake)
       if ($shake ne "");				# add water if present
     printf(LAMMPS "velocity        all create 0.0 12345678 dist uniform\n\n");
+    printf(LAMMPS "thermo          1\n");		# set thermo style
+    printf(LAMMPS "thermo_style    multi\n");
+    printf(LAMMPS "timestep        0.5\n\n");		# 0.5 ps time step
     printf(LAMMPS "restart         10 $project.restart1 $project.restart2\n");
     printf(LAMMPS "dump            1 all atom 10 $project.dump\n");
     printf(LAMMPS "dump_modify     1 image yes scale yes\n\n");
@@ -1463,6 +1497,972 @@
     close(LAMMPS);
   }
 
+ # ------------------ DESCRIPTION: sub DihedralCorrect6Ring ------------------ #
+ #                                                                             #
+ # This subroutine is a subsequent correction of the dihedral 1-4 non-bonded   #
+ # interaction scaling factor in the LAMMPS data file. The problem occurs in   #
+ # dealing with carbohydrate systems, when some dihedrals outside of a 6-ring  #
+ # are incorrectly assigned to the same dihedral type as dihedrals within a    #
+ # 6-ring. Thus, those dihedrals outside of a 6-ring will be treated with a    #
+ # 1-4 non-bonded interaction scaling factor of 0.5 instead of 1.              #
+ #                                                                             #
+ # By:   Xiaohu Hu (hux2@ornl.gov)                                             #
+ #                                                                             #
+ # April 2009                                                                  #
+ #                                                                             #
+ # --------------------------------------------------------------------------- #
+
+sub DihedralCorrect6Ring
+{
+	print "\nINITIATE DIHEDRAL CORRECTION...\n\n";
+	## Variables for general data
+	# arrays
+	my @temp_data1;
+	my @temp_data2;
+	my @dihedral_coeffs;
+	my @dihedral_list;
+	my @raw_data;
+	my @temp1;
+	my @temp2;
+	my @temp3;
+	my @ring_dihe_list;
+	my @ring_dihetype_list;
+	
+	# integers
+	my $counter1 = 0;
+	my $counter2 = 0;
+	my $net_ndihedral = 0;
+	my $net_ndihedral_types = 0;
+	my $splice_onset_dihe = 0;
+	my $splice_onset_dihe_coeff = 0;
+	my $n;
+	my $ntyp;
+
+	# matrix
+	my @dihedral_matrix;
+	my @dihedral_coeff_matrix;
+	my @new_dihedral_coeff_matrix;
+	my @new_dihedral_matrix;
+
+	## Variables for dihedral matrix data
+	# "Dihedral Coeffs"
+	my $dihedral_type_c;
+	my $amp;
+	my $period;
+	my $equ_val;
+	my $scaling;
+
+	# "Dihedrals"
+	my $dihedral_no;
+	my $dihedral_type_l;
+	my $atom_1_no;
+	my $atom_2_no;
+	my $atom_3_no;
+	my $atom_4_no;
+
+# ------------- Reread the previously generated LAMMPS data file --------------------
+
+	open(LAMMPS, "< $project.data") or 
+	die "\"sub DihedralCorrect6Ring\" cannot open \"$project.data!\n";
+	print "Analysing \"$project.data\"...\n\n";
+	@raw_data = <LAMMPS>;
+	close(LAMMPS);
+	
+	# Find the number of dihedrals and dihedral types and the sections "Dihedrals" 
+	# and "Dihedral Coeffs" in LAMMPS data file
+	foreach $line (@raw_data) {
+	   $counter1++;
+	   chomp($line);
+	   if ($line =~ m/dihedrals/) {
+		  ($n,$string) = split(" ",$line);
+		  print "$n dihedrals\n";
+	   }
+	   if ($line =~ m/dihedral types/) {
+		   ($ntyp,$string) = split(" ",$line);
+		   print "$ntyp dihedral types\n";
+	   }
+	   if ($line =~ m/Dihedral Coeffs/) {
+	     print "Section \"Dihedrals\" found\n";
+	     $splice_onset_dihe_coeff = $counter1;
+     	   }
+	   if ($line =~ m/Dihedrals/) {
+	     print "Section \"Dihedral Coeffs\" found\n";
+	     $splice_onset_dihe = $counter1;
+	   }
+	}
+	if ($splice_onset_dihe_coeff == 0 and $splice_onset_dihe == 0) {
+		print "\nNo dihedral data in \"$project.data\", no dihedral correction necessary\n";
+		return;
+	}
+	elsif ($splice_onset_dihe_coeff == 0 or $splice_onset_dihe == 0) {
+		print "\nDihedral data incomplete! Dihedral correction impossible\n";
+		return;
+	}
+
+
+# --------------- Transform the raw data into matrices -----------------------
+
+	@temp_data1 = @temp_data2 = @raw_data;
+
+	#Store the section "Dihedral Coeffs" into a new list
+	@dihedral_coeffs = splice(@temp_data1,$splice_onset_dihe_coeff,$ntyp+1);
+
+	# Transfer the data from "@dihedral_coeffs" (an array of strings) 
+	# into "@dihedral_coeff_matrix" (a 6 x $n matrix of integers)
+	for (@dihedral_coeffs) {
+		($dihedral_type_c,
+		 $amp,
+		 $period,
+		 $equ_val,
+		 $scaling) = split(" ");
+
+	 	push(@dihedral_coeff_matrix, 
+		     [$dihedral_type_c,
+		      $amp,
+		      $period,
+		      $equ_val,
+		      $scaling]);
+ 	}
+
+	# Store the section "Dihedrals" into a new list
+	@dihedral_list = splice(@temp_data2,$splice_onset_dihe,$n+1);
+
+	# Transfer the data from "@dihedral_list" (an array of strings) 
+	# into "@dihedral_matrix" (a 6 x $n matrix of integers)
+	for (@dihedral_list) {
+		($dihedral_no,
+		 $dihedral_type_l,
+		 $atom_no_1,
+		 $atom_no_2,
+		 $atom_no_3,
+		 $atom_no_4) = split(" ");
+
+	 	push(@dihedral_matrix, 
+		     [$dihedral_no,
+		      $dihedral_type_l,
+		      $atom_no_1,
+		      $atom_no_2,
+		      $atom_no_3,
+		      $atom_no_4]);
+	}
+
+	for (my $i = 1; $i < $n; $i++) {
+		my $cur_type = ${$dihedral_matrix[$i]}[1];
+		if ($cur_type == 1 or 
+			$cur_type == 16 or
+			$cur_type == 34 or 
+			$cur_type == 46 or 
+			$cur_type == 58 or
+		       $cur_type == 64) {
+		       push(@list,$cur_type);
+	       }
+       }
+       @list = sort {$a <=> $b} @list;
+       #print "@list\n";
+       #print "Total: $#list\n";
+
+# ------------------ Reformat the matrices -------------------------------
+
+	# Loop the dihedral coefficient matrix and throw away all elements
+	# with a zero scaling factor (= entries with periodicity != 1)
+	for (my $i = 1; $i < $ntyp; $i++) {
+		my $current_sf = ${$dihedral_coeff_matrix[$i]}[4];
+		if ($current_sf != 0) {
+			push(@new_dihedral_coeff_matrix,
+				[${$dihedral_coeff_matrix[$i]}[0],
+				${$dihedral_coeff_matrix[$i]}[1],
+		     		${$dihedral_coeff_matrix[$i]}[2],
+		     		${$dihedral_coeff_matrix[$i]}[3],
+		     		${$dihedral_coeff_matrix[$i]}[4]]);
+			$net_ndihedral_types++;
+	   }
+   	}
+
+	# Remove the duplicated dihedrals from the @dihedral_matrix and save
+	# results into @new_dihedral_matrix
+	push(@new_dihedral_matrix,
+		[${$dihedral_matrix[1]}[0],
+		${$dihedral_matrix[1]}[1],
+		${$dihedral_matrix[1]}[2],
+		${$dihedral_matrix[1]}[3],
+		${$dihedral_matrix[1]}[4],
+		${$dihedral_matrix[1]}[5]]);
+	$net_ndihedral = 1;
+	for (my $i = 2; $i < $n; $i++) {
+		if (${$dihedral_matrix[$i]}[2] != ${$dihedral_matrix[$i-1]}[2] or
+			${$dihedral_matrix[$i]}[3] != ${$dihedral_matrix[$i-1]}[3] or
+			${$dihedral_matrix[$i]}[4] != ${$dihedral_matrix[$i-1]}[4] or
+			${$dihedral_matrix[$i]}[5] != ${$dihedral_matrix[$i-1]}[5]) {
+			push(@new_dihedral_matrix,
+				[${$dihedral_matrix[$i]}[0],
+				${$dihedral_matrix[$i]}[1],
+				${$dihedral_matrix[$i]}[2],
+				${$dihedral_matrix[$i]}[3],
+				${$dihedral_matrix[$i]}[4],
+				${$dihedral_matrix[$i]}[5]]);
+			$net_ndihedral++;
+		}
+	}
+
+	# Print out the matrix
+	# my $ref_line;
+	# my $column;
+	# print "New dihedral list:\n";
+	# foreach $ref_line (@new_dihedral_matrix) {
+	#	foreach $column (@$ref_line) {
+	#		print "$column " 
+	#	}
+	#	print "\n";
+	# }
+
+# --------------- Seach for the wrong scaling factors ----------------------------
+
+	# Loop through the dihedral matrix to determine the dihedrals within 
+	# a 6-ring. Note there is some duplication in this approach due to 
+	# processing already processed dihedrals. This will be taken care of 
+	# later.
+	#
+	# NOTE: @ringlist contains the dihedrals types which corresponds to
+	# dihedrals within a 6-ring system.
+	#
+	my $n6ring = 0;
+	for (my $i = 1; $i < $net_ndihedral; $i++) {
+		my $current_i = ${$new_dihedral_matrix[$i]}[2];
+		my $current_l = ${$new_dihedral_matrix[$i]}[5];
+		for (my $j = $i + 1; $j < $net_ndihedral; $j++) {
+			if ( ($current_i == ${$new_dihedral_matrix[$j]}[2] and 
+					$current_l == ${$new_dihedral_matrix[$j]}[5]) or 
+				($current_i == ${$new_dihedral_matrix[$j]}[5] and 
+					$current_l == ${$new_dihedral_matrix[$j]}[2]) ) {
+				push(@temp2,${$new_dihedral_matrix[$i]}[0]);
+				push(@temp2,${$new_dihedral_matrix[$j]}[0]);
+				push(@temp3,${$new_dihedral_matrix[$i]}[1]);
+				push(@temp3,${$new_dihedral_matrix[$j]}[1]);
+				$n6ring++;
+			}
+		}
+	}
+
+	if ($n6ring == 0) {
+		print "\nNo dihedrals within 6-ring structure found. No correction necessary.\n";
+		return;
+	}
+
+	# Sort the lists according to the numerical order
+	@ring_dihe_list = sort {$a <=> $b} @temp2;
+	@ring_dihetype_list = sort {$a <=> $b} @temp3;
+
+	# Remove the dups
+	my %seen1;
+	for (my $i = 0; $i <= $#ring_dihe_list;) {
+		splice @ring_dihe_list, --$i, 1
+		if $seen1 {$ring_dihe_list[$i++]}++;
+	}
+
+	my %seen2;
+	for (my $i = 0; $i <= $#ring_dihetype_list;) {
+		splice @ring_dihetype_list, --$i, 1
+		if $seen1 {$ring_dihetype_list[$i++]}++;
+	}
+	
+	print "6-ring dihedral types:\n";
+	print "@ring_dihetype_list\n";
+	print "6-ring dihedrals:\n";
+	print "@ring_dihe_list\n";
+
+	# Locate the wrong dihedrals in the dihedral list. Criteria to be wrong:
+	# if the type of the dihedral is equal to one from the list @ring_dihetype_list
+	# but not one from the @ring_dihe_list
+	my @errorlist;
+	my @errortypes;
+	my @raw_errortypes;
+	my $dihe_flag = 0;
+
+	for (my $i = 1; $i < $n; $i++) {
+		my $cur_dihe = ${dihedral_matrix[$i]}[0];
+		my $cur_type = ${dihedral_matrix[$i]}[1];
+		
+		for (my $j = 0; $j <= $#ring_dihetype_list; $j++) {
+			if ($cur_type == $ring_dihetype_list[$j]) {
+				for (my $k = 0; $k <= $#ring_dihe_list; $k++) {
+					if ($cur_dihe == $ring_dihe_list[$k]) {
+						$dihe_flag++;
+					}
+				}
+		       	}
+		}
+
+		if ($dihe_flag == 0) {
+			for (my $j = 0; $j <= $#ring_dihetype_list; $j++) {
+				if ($cur_type == $ring_dihetype_list[$j]) {
+					push(@errorlist,$cur_dihe);
+					push(@raw_errortypes,$cur_type);
+					$counter2++;
+				}
+			}
+		}
+
+		$dihe_flag = 0;
+	}
+
+	if ($counter2 == 0) {
+		print "\nNo mis-assigned dihedrals found. No correction necessary.\n";
+		return;
+	}
+
+	print "mis-assigned dihedral/s found: $counter2\n";
+	print "@errorlist\n";
+	# print "@raw_errortypes\n";
+
+	# Sort the @errortypes and remove dups
+	@errortypes = sort {$a <=> $b} @raw_errortypes;
+	my %seen4;
+	for (my $i = 0; $i <= $#errortypes;) {
+		splice @errortypes, --$i, 1
+		if $seen4 {$errortypes[$i++]}++;
+	}
+
+	print "associated dihedral type/s\n";
+	print "@errortypes\n";
+
+# ------------ Add new dihedral types for the mis-assigned dihedrals -----------
+	
+	print "\nWriting \"corrected_$project.data\"...\n\n";
+	open(REWRITE,"> corrected_$project.data")
+		or die "Can not write file \"corrected_$project.data\"!\n";
+
+	my $counter3 = 0;
+	my $fix_start = $splice_onset_dihe_coeff + $ntyp + 1;
+	my $new_ntyp = $ntyp + $#errortypes +1;
+
+	foreach $line (@raw_data) {
+		# update header information
+		if ($line =~ m/dihedral types/) {
+			$line =~ s/$ntyp/$new_ntyp/;
+		}
+
+		$counter3++;
+		printf(REWRITE "$line\n");
+		if ($counter3 == $fix_start) { last }
+	}
+
+	my @newtypes;
+	for (my $i = 0; $i <= $#errortypes; $i++) {
+		$ntyp++;
+		printf(REWRITE "%8d %10.7g %10d %10d          1\n",
+			$ntyp,
+			${$dihedral_coeff_matrix[$errortypes[$i]]}[1],
+			${$dihedral_coeff_matrix[$errortypes[$i]]}[2],
+			${$dihedral_coeff_matrix[$errortypes[$i]]}[3]);
+		print "New dihedral type $ntyp added\n";
+		push(@newtypes,$ntyp);
+	}
+
+# ------------ Assign the wrong dihedrals with the new types ----------------
+
+	print "\nCorrecting the mis-assigned dihedrals...\n\n";
+
+	printf(REWRITE "$raw_data[$splice_onset_dihe - 2]\n");
+	printf(REWRITE "$raw_data[$splice_onset_dihe - 1]\n");
+
+	# Overwrite the wrong dihedrals in the dihedral list (section "Dihedrals")
+	my $counter3 = -1;
+	my $write_flag = 0;
+	my @temp_line;
+
+	for ($j = $splice_onset_dihe; $j <= $#raw_data; $j++) {
+		$counter3++;
+		for (my $i = 0; $i <= $#errorlist; $i++) {
+			if ($counter3 == $errorlist[$i]) {
+				@temp_line = split(" ",$raw_data[$j]);
+				for (my $k = 0; $k <= $#errortypes; $k++) {
+					if ($temp_line[1] == $errortypes[$k]) {
+						printf(REWRITE "%8d %7d %7d %7d %7d %7d\n",
+						${$dihedral_matrix[$errorlist[$i]]}[0],
+						$newtypes[$k],
+						${$dihedral_matrix[$errorlist[$i]]}[2],
+						${$dihedral_matrix[$errorlist[$i]]}[3],
+						${$dihedral_matrix[$errorlist[$i]]}[4],
+						${$dihedral_matrix[$errorlist[$i]]}[5]);
+					print "Dihedral No. ${$dihedral_matrix[$errorlist[$i]]}[0] corrected\n";
+					$write_flag = 1;
+					}
+				}
+			}
+		}
+		if ($write_flag == 0) { printf(REWRITE "$raw_data[$j]\n");}
+		$write_flag = 0;
+	}
+
+	print "\nDONE!\n";
+
+	close(REWRITE);
+
+# End of the subroutine
+}
+
+# ----------------------- DESCRIPTION: sub CharmmCmap ------------------------ #
+# This subroutine add a new section "CMAP" to the LAMMPS data file, which      #
+# a part of the implementation of "CHARMM CMAP" (see references) in LAMMPS.    #
+# The section "CMAP" contains a list of dihedral ID pairs from adjecent        #
+# peptide backtone dihedrals whose dihedral angles are corrresponding to PHI   #
+# and PSI. (PHI: C--N--C_aphla_C and PSI: N--C_alpha--C--N)                    #
+#                                                                              #
+# By:   Xiaohu Hu (hux2@ornl.gov)                                              #
+# May 2009                                                                     #
+#                                                                              #
+# Modified May 2013 by: Robert Latour (latourr@clemson.edu) and                #
+#                       Chris Lorenz (chris.lorenz@kcl.ac.uk                   #
+#                                                                              #
+# References:                                                                  #
+# - MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Improved Treatment of   #
+#   Protein Backbone Conformational in Empirical Force Fields, J. Am. Chem.    #
+#   Soc. 126(2004): 698-699.                                                   #
+# - MacKerell, A.D., Jr., Feig, M., Brooks, C.L., III, Extending the Treatment #
+#   of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase   #
+#   Quantum Mechnacis in Reproducing Protein Conformational Distributions in   #
+#   Molecular Dynamics Simulations, J. Comput. Chem. 25(2004): 1400-1415.      #
+# ---------------------------------------------------------------------------- #
+
+sub CharmmCmap 
+{
+	print "\nINITIATING CHARMM CMAP SUBROUTINE...\n\n";
+
+	# Reread and analyse $project.data
+	my @raw_data;
+	open(LAMMPS, "< $project.data") or
+	die "\"sub CharmmCmap()\" cannot open \"$project.data!\n";
+	print "Analyzing \"$project.data\"...\n\n";
+	@raw_data = <LAMMPS>;
+	close(LAMMPS);
+
+	# Locate and extract the sections "Masses" and "Atoms"
+	my $line_number = 0;
+	# Header infos, 0 by default
+	my $natom_types = 0;
+	my $natom_number = 0;
+	my $ndihedral_number = 0;
+	my $temp_string;
+	# splice points, 0 by default
+	my $splice_onset_masses = 0;
+	my $splice_onset_atoms = 0;
+	my $splice_onset_dihedrals = 0;
+
+	foreach my $line (@raw_data) {
+		$line_number++;
+		chomp($line);
+	# Extract useful informations from the header
+		if ($line =~ m/atom types/) {
+			($natom_types,$temp_string) = split(" ",$line);
+			if ($natom_types == 0) {
+				die "\nError: Number of atom types is 0!\n";
+			}
+			print "Total atom types: $natom_types\n";
+		}
+		if ($line =~ m/atoms/) {
+			($natom_number,$temp_string) = split(" ",$line);
+			if ($natom_number == 0) {
+				die "\nError: Number of atoms is 0!\n";
+			}
+			print "Total atoms: $natom_number\n";
+		}
+		if ($line =~ m/dihedrals/) {
+			($ndihedral_number,$temp_string) = split(" ",$line);
+			if ($ndihedral_number == 0) {
+				die "\nError: Number of dihedrals is 0\n";
+			}
+			print "Total dihedrals: $ndihedral_number\n";
+		}
+	# Locate and data from sections "Masses", "Atoms" and "Dihedrals"
+		if ($line =~ m/Masses/) {
+			$splice_onset_masses = $line_number + 1;
+			if ($splice_onset_masses-1 == 0) {
+				die "\nError: Can not find the section \"Masses\"\n";
+			}
+			print "Section \"Masses\" found: line $splice_onset_masses\n";
+		}
+		if ($line =~ m/Atoms/) {
+			$splice_onset_atoms = $line_number +1;
+			if ($splice_onset_atoms-1 == 0) {
+				die "\nError: Can not find the section \"Atoms\"\n";
+			}
+			print "Section \"Atoms\" found: line $splice_onset_atoms\n";
+		}
+		if ($line =~ m/Dihedrals/) {
+			$splice_onset_dihedrals = $line_number + 1;
+			if ($splice_onset_dihedrals-1 == 0) {
+				die "\nError: Can not find the section \"Dihedrals\"\n";
+			}
+			print "Section \"Dihedrals\" found: line $splice_onset_dihedrals\n";
+		}
+	}
+
+	print "\nGenerating PHI/PSI dihedral pair list...\n\n";
+
+	my @temp1 = @raw_data;
+	my @temp2 = @raw_data;
+	my @temp3 = @raw_data;
+
+	# Extract the section "Masses", "Atoms" and "Dihedrals"
+	my @temp_masses_data = splice(@temp1,$splice_onset_masses,$natom_types);
+	my @temp_atoms_data = splice(@temp2,$splice_onset_atoms,$natom_number);
+	my @temp_dihedrals_data = splice(@temp3,$splice_onset_dihedrals,$ndihedral_number);
+	
+	# Store @temp_masses_dat into a matrix
+	my @masses_matrix;
+	my $atom_type;
+	my $mass;
+	for (@temp_masses_data) {
+		($atom_type, $mass) = split(" ");
+		push(@masses_matrix,[$atom_type,$mass]);
+	}
+
+	# Store @temp_atoms_data into a matrix
+	my @atoms_matrix;
+	my $atom_ID;
+	my $molecule_ID;
+	my $atype;
+	my $charge;
+	my $atom_x_coor;
+	my $atom_y_coor;
+	my $atom_z_coor;
+	for (@temp_atoms_data) {
+		($atom_ID,$molecule_ID,$atype,$charge,$atom_x_coor,$atom_y_coor,$atom_z_coor) = split(" ");
+	 	push(@atoms_matrix,
+			[$atom_ID,$molecule_ID,$atype,$charge,$atom_x_coor,$atom_y_coor,$atom_z_coor]);
+	}
+
+	# Store @temp_dihedrals_data into a matrix
+	my @dihedrals_matrix;
+	my $dihedral_ID;
+	my $dihedtal_type;
+	my $dihe_atom1;
+	my $dihe_atom2;
+	my $dihe_atom3;
+	my $dihe_atom4;
+	for (@temp_dihedrals_data) {
+		($dihedral_ID,$dihedral_type,$dihe_atom1,$dihe_atom2,$dihe_atom3,$dihe_atom4) = split(" ");
+		push(@dihedrals_matrix,
+			[$dihedral_ID,$dihedral_type,$dihe_atom1,$dihe_atom2,$dihe_atom3,$dihe_atom4]);
+	}
+	
+	# Find out and extract the peptide backbone dihedrals
+	#
+	# Definitions of peptide backbone dihedrals
+	#
+	# For dihedral angle PHI: C--N--CA--C
+	# For dihedral angle PSI: N--CA--C--N
+	#
+	# ---------------------------------------------------------
+	#  atom  |  mass  |partial charge|     amino-acid
+	# ---------------------------------------------------------
+	#   C    | 12.011 |     0.51     | all except GLY and PRO
+	#   N    | 14.007 |    -0.29     | PRO
+	#   N    | 14.007 |    -0.47     | all except PRO
+	#   CA   | 12.011 |     0.07     | all except GLY and PRO
+	#   CA   | 12.011 |    -0.02     | GLY
+	#   CA   | 12.011 |     0.02     | PRO
+	# ---------------------------------------------------------
+	#
+	#  Peptide backbone
+	#        ...
+	#         /
+	#      O=C
+	#         \
+	#          N-H
+	#         / -----> PHI (C-N-CA-C)
+	#      H-CA-R
+	#         \ -----> PSI (N-CA-C-N)
+	#          C=O
+	#         /
+	#      H-N
+	#         \
+	#         ...
+	#
+	# Criteria to be a PHI/PSI dihedral pair:
+	# 1. Atoms have to match with the mass/charge constellations as 
+	#    defined above.
+	# 2. The atoms N--CA--C needs to be covalently bonded with each
+	#    other.
+
+	# Find which types do C, N and CA correspond to and store them
+	# in lists
+	my $mass_carbon = 12.011;
+	my $mass_nitrogen = 14.007;
+
+	my @carbon_list;
+	my @nitrogen_list;
+	my $carbon_counter = 0;
+	my $nitrogen_counter = 0;
+
+	for (my $i = 0; $i < $natom_types; $i++) {
+		if (${$masses_matrix[$i]}[1] == $mass_carbon) {
+			push(@carbon_list,${$masses_matrix[$i]}[0]);
+			$carbon_counter++;
+		}
+		if (${$masses_matrix[$i]}[1] == $mass_nitrogen) {
+			push(@nitrogen_list,${$masses_matrix[$i]}[0]);
+			$nitrogen_counter++;
+		}
+	}
+	# Quit if no carbons or nitrogens
+	if ($carbon_counter == 0 or $nitrogen_counter == 0) {
+		if ($carbon_counter == 0) {
+			print "No carbon atoms exist in the system\n";
+		}
+		if ($nitrogen_counter == 0) {
+			print "No nitrogen atoms exist in the system\n";
+		}
+		print "CMAP usage impossible\n";
+		return;
+	}
+
+	print "Carbon atom type/s: @carbon_list\n";
+	print "Nitrogen atom type/s: @nitrogen_list\n";
+
+	# Determine the atom types of C, CA and N
+
+	# Charges of the backbone atoms
+	my $charge_C = 0.51;
+	my $charge_CA = 0.07;
+	my $charge_N = -0.47;
+
+	# Special setting for PRO
+	my $charge_N_PRO = -0.29;
+	my $charge_CA_PRO = 0.02;
+
+	# Special setting for GLY
+	my $charge_CA_GLY = -0.02;
+
+	# Peptide backbone atom types
+	my $C_type;
+	my $CA_type;
+	my $CA_GLY_type;
+	my $CA_PRO_type;
+	my $N_type;
+	my $N_PRO_type;
+
+	my $C_counter = 0;
+	my $CA_counter = 0;
+	my $CA_GLY_counter = 0;
+	my $CA_PRO_counter = 0;
+	my $N_counter = 0;
+	my $N_PRO_counter = 0;
+
+	my $C_flag = 0;
+ 
+	for (my $i = 0; $i <= $natom_number; $i++) {
+		my $cur_type = ${$atoms_matrix[$i]}[2];
+		my $cur_charge = ${$atoms_matrix[$i]}[3];
+		for (my $j = 0; $j <= $#carbon_list; $j++) {
+			if ($cur_type == $carbon_list[$j]) {
+				$C_flag = 1;
+				if ($cur_charge == $charge_C) {
+					$C_type = $cur_type;
+					$C_counter++;
+				}
+				if ($cur_charge == $charge_CA) {
+					$CA_type = $cur_type;
+					$CA_counter++;
+				}
+				if ($cur_charge == $charge_CA_GLY) {
+					$CA_GLY_type = $cur_type;
+					$CA_GLY_counter++;
+				}
+				if ($cur_charge == $charge_CA_PRO) {
+					$CA_PRO_type = $cur_type;
+					$CA_PRO_counter++;
+				}
+			}
+		}
+		if ($C_flag == 0) {
+			for (my $k = 0; $k <= $#nitrogen_list; $k++) {
+				if ($cur_type == $nitrogen_list[$k]) {
+					if ($cur_charge == $charge_N) {
+						$N_type = $cur_type;
+						$N_counter++;
+					}
+					if ($cur_charge == $charge_N_PRO) {
+						$N_PRO_type = $cur_type;
+						$N_PRO_counter++;
+					}
+				}
+			}
+		}
+		$C_flag = 0;
+	}
+
+	# Quit if one of the atom types dosen't exist
+	if ( $C_counter == 0 or 
+	    ($CA_counter == 0 and $CA_GLY_counter == 0 and $CA_PRO_counter == 0) or 
+	    ($N_counter == 0 and $N_PRO_counter == 0) ) {
+		if ($C_counter == 0) {
+			print "\nCannot find the peptide backbone C atom type\n";
+		}
+		if ($CA_counter == 0 and $CA_GLY_counter == 0 and $CA_PRO_counter == 0) {
+			print "\nCannot find the peptide backbone C-alpha atom type\n";
+		}
+		if ($N_counter == 0 and $N_PRO_counter == 0) {
+			print "\nCannot find the peptide backbone N atom type\n";
+		}
+		print "CMAP usage impossible\n";
+		return;
+	}
+
+	print "Peptide backbone carbon type: $C_type\n";
+	print "Alpha-carbon type: $CA_type\n" if ($CA_counter > 0);
+	print "Alpha-carbon type (GLY): $CA_GLY_type\n" if ($CA_GLY_counter > 0);
+	print "Alpha-carbon type (PRO): $CA_PRO_type\n" if ($CA_PRO_counter > 0);
+	print "Peptide backbone nitrogen type: $N_type\n" if ($N_counter >0);
+	print "Peptide backbone nitrogen type (PRO): $N_PRO_type\n" if ($N_PRO_counter > 0);
+
+	# Loop through the dihedral list to find the PHI- and PSI-dihedrals
+	my @PHI_dihedrals;
+	my @PSI_dihedrals;
+	my $PHI_counter = 0;
+	my $PSI_counter = 0;
+
+	for (my $i = 0; $i < $ndihedral_number; $i++) {
+		my $cur_dihe_ID = ${dihedrals_matrix[$i]}[0];
+		my $cur_atom1_type = ${atoms_matrix[${dihedrals_matrix[$i]}[2]-1]}[2];
+		my $cur_atom2_type = ${atoms_matrix[${dihedrals_matrix[$i]}[3]-1]}[2];
+		my $cur_atom3_type = ${atoms_matrix[${dihedrals_matrix[$i]}[4]-1]}[2];
+		my $cur_atom4_type = ${atoms_matrix[${dihedrals_matrix[$i]}[5]-1]}[2];
+
+		next if (${dihedrals_matrix[$i]}[2] == ${dihedrals_matrix[$i-1]}[2] and
+		         ${dihedrals_matrix[$i]}[3] == ${dihedrals_matrix[$i-1]}[3] and 
+	                 ${dihedrals_matrix[$i]}[4] == ${dihedrals_matrix[$i-1]}[4] and
+                         ${dihedrals_matrix[$i]}[5] == ${dihedrals_matrix[$i-1]}[5]);
+
+		# Determine PHI-dihedrals; If C-CA-N-C or C-N-CA-C, then save it in a list
+		if ($cur_atom1_type == $C_type and $cur_atom4_type == $C_type) {
+			if ( ( ($cur_atom2_type == $CA_type or 
+			        $cur_atom2_type == $CA_GLY_type or
+				$cur_atom2_type == $CA_PRO_type) and 
+			       ($cur_atom3_type == $N_type or
+			        $cur_atom3_type == $N_PRO_type) ) or 
+			     ( ($cur_atom3_type == $CA_type or 
+				$cur_atom3_type == $CA_GLY_type or
+			        $cur_atom3_type == $CA_PRO_type) and 
+			       ($cur_atom2_type == $N_type or 
+				$cur_atom2_type == $N_PRO_type) ) ) {
+				push (@PHI_dihedrals,$cur_dihe_ID);
+				$PHI_counter++;
+			}
+		}
+
+		# Determin PSI-dihedrals; If N-CA-C-N or N-C-CA-N (N can be both normal N or N proline),
+		# then save it in a list
+		if ( ($cur_atom1_type == $N_type and $cur_atom4_type == $N_type) or 
+		     ($cur_atom4_type == $N_PRO_type and $cur_atom1_type == $N_PRO_type) or
+	     	     ($cur_atom1_type == $N_type and $cur_atom4_type == $N_PRO_type) or
+                     ($cur_atom4_type == $N_type and $cur_atom1_type == $N_PRO_type) ) {
+			if ( ( ($cur_atom2_type == $CA_type or 
+			        $cur_atom2_type == $CA_GLY_type or
+		                $cur_atom2_type == $CA_PRO_type) and 
+			        $cur_atom3_type == $C_type) or
+			     ( ($cur_atom3_type == $CA_type or 
+				$cur_atom3_type == $CA_GLY_type or 
+			        $cur_atom3_type == $CA_PRO_type) and 
+				$cur_atom2_type == $C_type) ) {
+				push (@PSI_dihedrals,$cur_dihe_ID);
+				$PSI_counter++;
+			}
+		}
+	}
+
+	# Quit if no PHI or PSI dihedrals
+	if ($PHI_counter == 0 or $PSI_counter ==0) {
+		if ($PHI_counter == 0) {
+			print "Can not find the PHI backbone dihedrals\n";
+		}
+		if ($PSI_counter ==0) {
+			print "Can not find the PSI backbone dihedrals\n";
+		}
+		print "CMAP usage impossible\n";
+		return;
+	}
+
+	# Construct the PHI/PSI diheral pair list
+	#
+	# The algorithm:
+	#         _____
+	#        |     | 
+	#     1--2--3--4      PHI-dihedral
+	#     4--3--2--1
+	#   --C--N-CA--C--N-- Peptide backbone
+	#        1--2--3--4
+	#        4--3--2--1   PSI-dihedral
+	#        |_____|
+	#
+	# For a certain PHI dihedral, following conditions have to be met:
+	#
+	#        PHI         PSI
+	#  If (2--3--4) = (1--2--3)
+	#  or
+	#  if (2--3--4) = (4--3--2)
+	#  or
+	#  if (3--2--1) = (1--2--3)
+	#  or 
+	#  if (3--2--1) = (4--3--2),
+	#
+	# then these 2 dihedrals are a PHI/PSI pair. If a pair is found, the
+	# dihedral IDs will be stored in "@PHI_PSI_matrix".
+	
+	my @PHI_PSI_matrix;
+	my $crossterm_CA_charge;
+	my $crossterm_type;
+	my $crossterm_counter = 0;
+	my $crossterm_type1_flag = 0;
+        my $crossterm_type2_flag = 0;
+	my $crossterm_type3_flag = 0;
+	my $crossterm_type4_flag = 0;
+	my $crossterm_type5_flag = 0;
+	my $crossterm_type6_flag = 0;
+
+	for (my $i = 0; $i <= $#PHI_dihedrals; $i++) {
+		my $cur_PHI_dihe = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[0];
+		my $phi1 = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[2];
+		my $phi2 = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[3];
+		my $phi3 = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[4];
+		my $phi4 = ${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[5];
+		for (my $j = 0; $j <= $#PSI_dihedrals; $j++) {
+			my $cur_PSI_dihe = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[0];
+			my $psi1 = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[2];
+			my $psi2 = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[3];
+			my $psi3 = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[4];
+			my $psi4 = ${dihedrals_matrix[$PSI_dihedrals[$j]-1]}[5];
+			if ( ($phi2 == $psi1 and $phi3 == $psi2 and $phi4 == $psi3) or
+			     ($phi2 == $psi4 and $phi3 == $psi3 and $phi4 == $psi2) or
+			     ($phi3 == $psi1 and $phi2 == $psi2 and $phi1 == $psi3) or
+			     ($phi3 == $psi4 and $phi2 == $psi3 and $phi1 == $psi2) ) {
+
+			     # Find out to which amino acid the cross-term belongs
+
+			     if ($phi3 == $psi2 or $phi3 == $psi3) {
+				     $crossterm_CA_charge = ${atoms_matrix[${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[4]-1]}[3];
+			     }
+			     if ($phi2 == $psi2 or $phi2 == $psi3) {
+				     $crossterm_CA_charge = ${atoms_matrix[${dihedrals_matrix[$PHI_dihedrals[$i]-1]}[3]-1]}[3];
+			     }
+
+			     # Def. the type of the crossterm per cmap.data file; If C_alpha of the crossterm is
+			     # - ALA type, then $crossterm_type = 1;
+                             # - ALA-PRO (ALA is the current AA), then $crossterm_type = 2;
+			     # - PRO type, then $crossterm_type = 3;
+                             # - PRO-PRO (First PRO is the current AA), then $crossterm_type = 4;
+			     # - GLY type, then $crossterm_type = 5;
+                             # - GLY-PRO (GLY is the current AA), then $crossterm_type = 6;
+
+			     if ($crossterm_CA_charge == $charge_CA) { $crossterm_type = 1; $crossterm_type1_flag = 1; }
+			     if ($crossterm_CA_charge == $charge_CA_GLY) { $crossterm_type = 5; $crossterm_type5_flag = 1; }
+			     if ($crossterm_CA_charge == $charge_CA_PRO) { 
+					$crossterm_type = 3; $crossterm_type3_flag = 1;
+					# Checking the last crossterm, re-assign the last crossterm type if needed
+					if ($crossterm_counter-1 >= 0 and $PHI_PSI_matrix[$crossterm_counter-1][0] == 1) {
+						$PHI_PSI_matrix[$crossterm_counter-1][0] = 2;
+						$crossterm_type2_flag = 1;
+					}
+					if ($crossterm_counter-1 >= 0 and $PHI_PSI_matrix[$crossterm_counter-1][0] == 3) {
+                                                $PHI_PSI_matrix[$crossterm_counter-1][0] = 4;
+                                                $crossterm_type4_flag = 1;
+                                        }
+					if ($crossterm_counter-1 >= 0 and $PHI_PSI_matrix[$crossterm_counter-1][0] == 5) {
+                                                $PHI_PSI_matrix[$crossterm_counter-1][0] = 6;
+                                                $crossterm_type6_flag = 1;
+                                        }
+			     }	
+			     push(@PHI_PSI_matrix,[$crossterm_type,$phi1,$phi2,$phi3,$phi4,$psi4]);
+			     $crossterm_counter++;
+
+			     $crossterm_CA_charge = 0;
+			     $crossterm_type = 0;
+		     }
+		}
+	}
+
+	# Check whether the amino acid at the C-terminus is a PRO or not. If yes, the type of the last crossterm
+	# should be set to its X-PRO form  instead of X, where X is ALA, PRO, or GLY.  X-PRO form = X type + 1.
+
+	my @pdb_data;
+	open(PDB,"< $project.pdb")
+		or die "WARNING: Cannot open file \"$project.pdb\"! (required if the -cmap option is used)\n";
+	@pdb_data = <PDB>;
+	close(PDB);
+
+        my @ter_line;
+        my $ter_AA_type = 0;
+        my $ter_flag = 0;
+	foreach $line (@pdb_data) {
+		if ($line =~ m/TER/) {
+		      @ter_line = split(" ",$line);
+                      $ter_AA_type = $ter_line[2]; 	
+                      print "Terminal amino acid type is: $ter_AA_type\n";
+                      $ter_flag = 1;
+	        }
+        }
+        if ($ter_flag == 0) {
+                print "\n*** ERROR IN THE PDB FILE: ***\n";
+                print "In order for the CMAP section to be generated, the pdb file must \n";
+                print "identify the C-terminus amino acid in the file with 'TER'. \n";
+                print "This line is missing from the pdb file that was used.\n";
+                print "To correct this problem, open the pdb file in an editor,\n";
+                print "find the last atom of the last amino acid residue in the peptide\n";
+                print "chain and insert the following line immediately after that atom:\n";
+                print "                  'TER   <#1>   <RES>   <#2>' \n";
+                print "where '<#1> is the next atom number, <RES> is the three letter amino\n";
+                print "acid abbreviation for that amino acid, and <#2> is the molecule number\n";
+                print "of the terminal amino acid residue.\n\n";
+                print "For example, if the last atom of the last amino acid in the peptide\n";
+                print "sequence is listed in the pdb file as:\n\n"; 
+                print "  'ATOM   853  O  GLU  P  56  12.089 -1.695 -6.543 1.00 1.03  PROA'\n\n";
+                print "you would insert the following line after it:\n\n";
+                print "  'TER    854     GLU     56'\n\n";
+                print "If any additional atoms are listed in the pdb file (e.g., water, ions)\n";
+                print "after this terminal amino acid residue, their atom numbers and\n";
+                print "molecule numbers must be incremented by 1 to account for the new line\n";
+                print "that was inserted.\n\n";
+                die "Error: No terminating atom designated in pdb file!  See above note to correct problem.\n\n";
+        }
+
+        if ($ter_AA_type eq PRO) {
+                $PHI_PSI_matrix[$crossterm_counter-1][0] = $PHI_PSI_matrix[$crossterm_counter-1][0]+1;
+        }
+
+	# Print out PHI/PSI diheral pair list
+	my $pair_counter = 0;
+        # Don't presently use $ncrosstermtypes but have this available if wish to print it out
+	my $ncrosstermtypes = $crossterm_type1_flag + $crossterm_type2_flag + $crossterm_type3_flag + 
+                              $crossterm_type4_flag + $crossterm_type5_flag + $crossterm_type6_flag;
+	print "\nWriting \"$project.data\" with section \"CMAP crossterms\" added at the end.\n";
+	
+	# Writing the new lammps data file
+	open(REWRITE,"> $project.data")
+		or die "Cannot write file \"$project.data\"!\n";
+	foreach $line (@raw_data) {
+		printf(REWRITE "$line\n");
+		if ($line =~ m/impropers/) {
+			printf(REWRITE "%12d  crossterms\n", $crossterm_counter);
+		}
+	}
+	printf(REWRITE "CMAP\n\n");
+
+        my $ref_line;
+        my $column;
+	foreach $ref_line (@PHI_PSI_matrix) {
+		$pair_counter++;
+		printf(REWRITE "%8d",$pair_counter);
+		foreach $column (@$ref_line) {
+			printf(REWRITE " %7d",$column);
+		}
+		printf(REWRITE "\n");
+	}
+	close(REWRITE);
+
+	print "\nDone!\n\n";
+
+# End of the CharmmCmap subroutine
+}
 
 # main
 
@@ -1470,4 +2470,6 @@
   WriteData();
   WriteLAMMPSInput();
   printf("Info: conversion complete\n\n") if ($info);
+  DihedralCorrect6Ring() if ($cdihedral);
+  CharmmCmap() if ($cmap);