Merge branch 'master' into feature_parameterupdate

doc/src/Build_extras.txt

@@ -642,30 +642,61 @@ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre
 
 USER-COLVARS package :h4,link(user-colvars)
 
+This package includes into the LAMMPS distribution the Colvars library, which
+can be built for the most part with all major versions of the C++ language.
+
+A few of the most recent features require C++11 support.  In particular, the
+library is optionally built together with the
+"Lepton"_https://simtk.org/projects/lepton library, a copy of which is also
+included in the LAMMPS distribution.  Lepton implements the
+"customFunction"_http://colvars.github.io/colvars-refman-lammps/colvars-refman-lammps.html#colvar|customFunction
+feature, and requires C++11 support.
+
+See "here"_https://colvars.github.io/README-c++11.html for a detailed list of
+C++11-only features.
+
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_USER-COLVARS=yes".
+This is the recommended build recipe: no additional settings are normally
+needed besides "-D PKG_USER-COLVARS=yes".
+
+Building and linking of Lepton (or other C++11-only features) is enabled
+automatically when compilation is carried out with C++11 support, and disabled
+otherwise.  Optionally, Lepton build may be manually controlled with the flag
+"-D COLVARS_LEPTON=yes|no".
 
 [Traditional make]:
 
-Before building LAMMPS, you must build the COLVARS library in
-lib/colvars.  You can do this manually if you prefer; follow the
-instructions in lib/colvars/README.  You can also do it in one step
-from the lammps/src dir, using a command like these, which simply
-invoke the lib/colvars/Install.py script with the specified args:
+Before building LAMMPS, one must build the Colvars library in lib/colvars.
+
+This can be done manually in the same folder by using or adapting one of the
+provided Makefiles: for example, Makefile.g++ for the GNU compiler.
+
+In general, it is safer to use build setting consistent with the rest of
+LAMMPS.  This is best carried out from the LAMMPS src directory using a
+command like these, which simply invoke the lib/colvars/Install.py script with
+the specified args:
 
 make lib-colvars                      # print help message
 make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
 make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
 make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre
 
-The build should produce two files: lib/colvars/libcolvars.a and
-lib/colvars/Makefile.lammps.  The latter is copied from an existing
-Makefile.lammps.* and has settings needed to build LAMMPS with the
-COLVARS library (though typically the settings are just blank).  If
-necessary, you can edit/create a new lib/colvars/Makefile.machine file
-for your system, which should define an EXTRAMAKE variable to specify
-a corresponding Makefile.lammps.machine file.
+The "machine" argument of the "-m" flag is used to find a Makefile.machine to
+use as build recipe.  If it does not already exist in lib/colvars, it will be
+auto-generated by using compiler flags consistent with those parsed from the
+core LAMMPS makefiles.
+
+Optional flags may be specified as environment variables:
+
+COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
+COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+
+The build should produce two files: the library lib/colvars/libcolvars.a
+(which also includes Lepton objects if enabled) and the specification file
+lib/colvars/Makefile.lammps.  The latter is auto-generated, and normally does
+not need to be edited.
+
 
 :line
 

doc/src/Build_settings.txt

@@ -38,11 +38,16 @@ when calling CMake.
 
 [CMake variable]:
 
--D DISABLE_CXX11_REQUIREMENT=yes
+-D DISABLE_CXX11_REQUIREMENT=yes :pre
+
+You can set additional C++ compiler flags (beyond those selected by CMake)
+through the CMAKE_CXX_FLAGS variable. Example for CentOS 7:
+
+-D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11" :pre
 
 [Makefile.machine setting]:
 
-LMP_INC = -DLAMMPS_CXX98
+LMP_INC = -DLAMMPS_CXX98 :pre
 
 :line
 

doc/src/Eqs/fix_bond_react.tex

@@ -0,0 +1,9 @@
+\documentstyle[12pt]{article}
+\pagestyle{empty}
+\begin{document}
+
+\begin{eqnarray*}
+   k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}
+\end{eqnarray*}                           
+
+\end{document}

doc/src/Errors_warnings.txt

@@ -390,6 +390,11 @@ have fully consistent image flags, since some bonds will cross
 periodic boundaries and connect two atoms with the same image
 flag. :dd
 
+{Increasing communication cutoff for GPU style} :dt
+
+The pair style has increased the communication cutoff to be consistent with
+the communication cutoff requirements for this pair style when run on the GPU. :dd
+
 {KIM Model does not provide 'energy'; Potential energy will be zero} :dt
 
 Self-explanatory. :dd

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="19 Sep 2019 version">
+<META NAME="docnumber" CONTENT="30 Oct 2019 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 @@
 :line
 
 LAMMPS Documentation :c,h1
-19 Sep 2019 version :c,h2
+30 Oct 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/PDF/pair_gayberne_extra.tex

@@ -48,8 +48,8 @@ $$ \mathbf{G}_{12} = \mathbf{A}_1^T \mathbf{S}_1^2 \mathbf{A}_1 +
 \mathbf{G}_2. $$
 
 Let the relative energy matrices $\mathbf{E}_i = \mbox{diag}
-(\epsilon_{ia}, \epsilon_{ib}, \epsilon_{ic})$ be given by 
-the relative well depths (dimensionless energy scales 
+(\epsilon_{ia}^{-1/\mu}, \epsilon_{ib}^{-1/\mu}, \epsilon_{ic}^{-1/\mu})$
+be given by the relative well depths (dimensionless energy scales 
 inversely proportional to the well-depths of the respective 
 orthogonal configurations of the interacting molecules). The 
 $\chi$ orientation-dependent energy based on the user-specified 
@@ -62,8 +62,8 @@ $$ \hat{\mathbf{r}}_{12} = { \mathbf{r}_{12} } / |\mathbf{r}_{12}|, $$
 
 and
 
-$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1^2 \mathbf{A}_1 +
-\mathbf{A}_2^T \mathbf{E}_2^2 \mathbf{A}_2 = \mathbf{B}_1 +
+$$ \mathbf{B}_{12} = \mathbf{A}_1^T \mathbf{E}_1 \mathbf{A}_1 +
+\mathbf{A}_2^T \mathbf{E}_2 \mathbf{A}_2 = \mathbf{B}_1 +
 \mathbf{B}_2. $$
 
 Here, we use the distance of closest approach approximation given by the
@@ -131,7 +131,7 @@ and
 
 $$ \frac{ \partial \chi_{12} }{ \partial \mathbf{q}_i } = 4.0 \cdot
 r^{-2} \cdot \mathbf{A}_i (- \mathbf{\iota}^T \cdot \mathbf{B}_i
-\times \mathbf{\iota} ). $$
+\times \mathbf{\iota} ) \cdot \mu \cdot \chi_{12}^{ ( \mu -1 ) / \mu}. $$
 
 For the derivative of the $\eta$ term, we were unable to find a matrix
 expression due to the determinant. Let $a_{mi}$ be the mth row of the

doc/src/compute_gyration_shape.txt

@@ -24,7 +24,7 @@ compute 1 molecule gyration/shape pe :pre
 
 Define a computation that calculates the eigenvalues of the gyration tensor of a
 group of atoms and three shape parameters. The computation includes all effects
-due to atoms passing thru periodic boundaries.
+due to atoms passing through periodic boundaries.
 
 The three computed shape parameters are the asphericity, b, the acylindricity, c,
 and the relative shape anisotropy, k:

doc/src/fix_bond_react.txt

@@ -266,7 +266,7 @@ either 'none' or 'charges.' Further details are provided in the
 discussion of the 'update_edges' keyword. The fourth optional section
 begins with the keyword 'Constraints' and lists additional criteria
 that must be satisfied in order for the reaction to occur. Currently,
-there are two types of constraints available, as discussed below.
+there are three types of constraints available, as discussed below.
 
 A sample map file is given below:
 
@@ -320,6 +320,27 @@ the central atom). Angles must be specified in degrees. This
 constraint can be used to enforce a certain orientation between
 reacting molecules.
 
+The constraint of type 'arrhenius' imposes an additional reaction
+probability according to the temperature-dependent Arrhenius equation:
+
+:c,image(Eqs/fix_bond_react.jpg)
+
+The Arrhenius constraint has the following syntax:
+
+arrhenius {A} {n} {E_a} {seed} :pre
+
+where 'arrhenius' is the required keyword, {A} is the pre-exponential
+factor, {n} is the exponent of the temperature dependence, {E_a} is
+the activation energy ("units"_units.html of energy), and {seed} is a
+random number seed. The temperature is defined as the instantaneous
+temperature averaged over all atoms in the reaction site, and is
+calculated in the same manner as for example
+"compute_temp_chunk"_compute_temp_chunk.html. Currently, there are no
+options for additional temperature averaging or velocity-biased
+temperature calculations. A uniform random number between 0 and 1 is
+generated using {seed}; if this number is less than the result of the
+Arrhenius equation above, the reaction is permitted to occur.
+
 Once a reaction site has been successfully identified, data structures
 within LAMMPS that store bond topology are updated to reflect the
 post-reacted molecule template. All force fields with fixed bonds,
@@ -395,7 +416,7 @@ will apply to all reactions.
 Computationally, each timestep this fix operates, it loops over
 neighbor lists (for bond-forming reactions) and computes distances
 between pairs of atoms in the list. It also communicates between
-neighboring processors to coordinate which bonds  are created and/or
+neighboring processors to coordinate which bonds are created and/or
 removed. All of these operations increase the cost of a timestep. Thus
 you should be cautious about invoking this fix too frequently.
 

doc/src/pair_oxdna.txt

@@ -23,7 +23,7 @@ style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxs
 style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
 args = list of arguments for these particular styles :ul
 
-  {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+  {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
     seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
     T = temperature (oxDNA units, 0.1 = 300 K)
     xi = temperature-independent coefficient in stacking strength
@@ -36,7 +36,7 @@ args = list of arguments for these particular styles :ul
 
 pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
 pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna/stk     seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -51,7 +51,10 @@ excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacki
 and coaxial stacking interaction {oxdna/coaxstk} as well
 as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
 opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
-are supported "(Sulc)"_#Sulc1.
+are supported "(Sulc)"_#Sulc1. Quasi-unique base-pairing between nucleotides can be achieved by using 
+more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
+This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
+up and down along the backbone.
 
 The exact functional form of the pair styles is rather complex.
 The individual potentials consist of products of modulation factors,

doc/src/pair_oxdna2.txt

@@ -24,7 +24,7 @@ style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/
 style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
 args = list of arguments for these particular styles :ul
 
-  {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+  {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
     seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
     T = temperature (oxDNA units, 0.1 = 300 K)
     xi = temperature-independent coefficient in stacking strength
@@ -41,7 +41,7 @@ args = list of arguments for these particular styles :ul
 
 pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
 pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
+pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
 pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
 pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
@@ -57,7 +57,10 @@ excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stac
 and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
 as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
 opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
-are supported "(Sulc)"_#Sulc2.
+are supported "(Sulc)"_#Sulc2. Quasi-unique base-pairing between nucleotides can be achieved by using 
+more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
+This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
+up and down along the backbone.
 
 The exact functional form of the pair styles is rather complex.
 The individual potentials consist of products of modulation factors,

doc/src/pair_zero.txt

@@ -71,9 +71,8 @@ This pair style writes its information to "binary restart
 files"_restart.html, so pair_style and pair_coeff commands do not need
 to be specified in an input script that reads a restart file.
 
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support the
-{inner}, {middle}, {outer} keywords.
+This pair style supports the use of the {inner}, {middle},
+and {outer} keywords of the "run_style respa"_run_style.html command.
 
 :line