Merge branch 'master' into refactor-reaxff-parser

doc/src/Packages_details.rst

@@ -311,6 +311,11 @@ rigid-body integrators with improved stability.
 
 **Author:** Oliver Henrich (University of Strathclyde, Glasgow).
 
+**Install:**
+
+The CG-DNA package requires that also the `MOLECULE <PKG-MOLECULE>`_ and
+`ASPHERE <PKG-ASPHERE>`_ packages are installed.
+
 **Supporting info:**
 
 * src/CG-DNA: filenames -> commands

doc/src/atom_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    atom_style style args
 
-* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
+* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
 
   .. parsed-literal::
 
@@ -110,6 +110,8 @@ quantities.
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *molecular*  | bonds, angles, dihedrals, impropers                 | uncharged molecules                  |
 +--------------+-----------------------------------------------------+--------------------------------------+
+| *oxdna*      | nucleotide polarity                                 | coarse-grained DNA and RNA models    |
++--------------+-----------------------------------------------------+--------------------------------------+
 | *peri*       | mass, volume                                        | mesoscopic Peridynamic models        |
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *smd*        | volume, kernel diameter, contact radius, mass       | solid and fluid SPH particles        |
@@ -193,6 +195,12 @@ position, which is represented by the eradius = electron size.
 For the *peri* style, the particles are spherical and each stores a
 per-particle mass and volume.
 
+The *oxdna* style is for coarse-grained nucleotides and stores the
+3'-to-5' polarity of the nucleotide strand, which is set through
+the bond topology in the data file. The first (second) atom in a
+bond definition is understood to point towards the 3'-end (5'-end)
+of the strand. Note that this style is part of the CG-DNA package.
+
 The *dpd* style is for dissipative particle dynamics (DPD) particles.
 Note that it is part of the DPD-REACT package, and is not for use with
 the :doc:`pair_style dpd or dpd/stat <pair_dpd>` commands, which can
@@ -323,10 +331,12 @@ INTEL, OPENMP, and OPT packages do not use accelerated atom
 styles.
 
 The accelerated styles are part of the KOKKOS package.  They are only
-enabled if LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` doc page for more info.
+enabled if LAMMPS was built with those packages.  See the :doc:`Build
+package <Build_package>` doc page for more info.
 
 You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+by including their suffix, or you can use the :doc:`-suffix command-line
+switch <Run_options>` when you invoke LAMMPS, or you can use the
 :doc:`suffix <suffix>` command in your input script.
 
 See the :doc:`Speed packages <Speed_packages>` doc page for more
@@ -339,7 +349,8 @@ This command cannot be used after the simulation box is defined by a
 :doc:`read_data <read_data>` or :doc:`create_box <create_box>` command.
 
 Many of the styles listed above are only enabled if LAMMPS was built
-with a specific package, as listed below.  See the :doc:`Build package <Build_package>` doc page for more info.
+with a specific package, as listed below.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 The *angle*\ , *bond*\ , *full*\ , *molecular*\ , and *template* styles are
 part of the MOLECULE package.
@@ -352,6 +363,8 @@ The *dipole* style is part of the DIPOLE package.
 
 The *peri* style is part of the PERI package for Peridynamics.
 
+The *oxdna* style is part of the CG-DNA package for coarse-grained simulation of DNA and RNA.
+
 The *electron* style is part of the EFF package for :doc:`electronic force fields <pair_eff>`.
 
 The *dpd* style is part of the DPD-REACT package for dissipative

doc/src/bond_oxdna.rst

@@ -76,6 +76,15 @@ commands:
    The coefficients in the above example have to be kept fixed and cannot
    be changed without reparameterizing the entire model.
 
+.. note::
+
+   This bond style has to be used with the *atom_style hybrid bond ellipsoid oxdna*
+   (see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
+   stores the 3'-to-5' polarity of the nucleotide strand, which is set through
+   the bond topology in the data file. The first (second) atom in a bond definition
+   is understood to point towards the 3'-end (5'-end) of the strand.
+
+
 Example input and data files for DNA and RNA duplexes can be found in
 examples/PACKAGES/cgdna/examples/oxDNA/ , /oxDNA2/ and /oxRNA2/.  A simple python
 setup tool which creates single straight or helical DNA strands, DNA/RNA
@@ -108,7 +117,7 @@ Related commands
 """"""""""""""""
 
 :doc:`pair_style oxdna/excv <pair_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
-:doc:`bond_coeff <bond_coeff>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+:doc:`bond_coeff <bond_coeff>`, :doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 
 Default
 """""""

doc/src/fix_gcmc.rst

@@ -451,6 +451,11 @@ When using fix gcmc in combination with fix shake or fix rigid,
 only GCMC exchange moves are supported, so the argument
 *M* must be zero.
 
+When using fix gcmc in combination with fix rigid, deletion
+of the last remaining molecule is not allowed for technical reasons,
+and so the molecule count will never drop below 1, regardless of the
+specified chemical potential.
+
 Note that very lengthy simulations involving insertions/deletions of
 billions of gas molecules may run out of atom or molecule IDs and
 trigger an error, so it is better to run multiple shorter-duration

doc/src/pair_oxdna.rst

@@ -91,6 +91,14 @@ for a detailed description of the oxDNA force field.
    or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
    the temperature coefficients have to be matched to the one used in the fix.
 
+.. note::
+
+   These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
+   (see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
+   stores the 3'-to-5' polarity of the nucleotide strand, which is set through
+   the bond topology in the data file. The first (second) atom in a bond definition
+   is understood to point towards the 3'-end (5'-end) of the strand.
+
 Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/.
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/.
@@ -120,7 +128,7 @@ Related commands
 :doc:`bond_style oxdna/fene <bond_oxdna>`, :doc:`pair_coeff <pair_coeff>`,
 :doc:`bond_style oxdna2/fene <bond_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`,
 :doc:`bond_style oxrna2/fene <bond_oxdna>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
-:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+:doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 
 Default
 """""""

doc/src/pair_oxdna2.rst

@@ -100,6 +100,14 @@ and  :ref:`(Ouldridge) <Ouldridge2>` for a detailed description of the oxDNA2 fo
    e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
    the temperature coefficients have to be matched to the one used in the fix.
 
+.. note::
+
+   These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
+   (see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
+   stores the 3'-to-5' polarity of the nucleotide strand, which is set through
+   the bond topology in the data file. The first (second) atom in a bond definition
+   is understood to point towards the 3'-end (5'-end) of the strand.
+
 Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/.
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/.
@@ -127,7 +135,7 @@ Related commands
 :doc:`bond_style oxdna2/fene <bond_oxdna>`, :doc:`pair_coeff <pair_coeff>`,
 :doc:`bond_style oxdna/fene <bond_oxdna>`, :doc:`pair_style oxdna/excv <pair_oxdna>`,
 :doc:`bond_style oxrna2/fene <bond_oxdna>`, :doc:`pair_style oxrna2/excv <pair_oxrna2>`,
-:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+:doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 
 Default
 """""""

doc/src/pair_oxrna2.rst

@@ -101,6 +101,14 @@ and  :ref:`(Ouldridge) <Ouldridge3>` for a detailed description of the oxRNA2 fo
    e.g. through :doc:`fix langevin <fix_langevin>` or :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
    the temperature coefficients have to be matched to the one used in the fix.
 
+.. note::
+
+   These pair styles have to be used with the *atom_style hybrid bond ellipsoid oxdna*
+   (see documentation of :doc:`atom_style <atom_style>`). The *atom_style oxdna*
+   stores the 3'-to-5' polarity of the nucleotide strand, which is set through
+   the bond topology in the data file. The first (second) atom in a bond definition
+   is understood to point towards the 3'-end (5'-end) of the strand.
+
 Example input and data files for DNA duplexes can be found in examples/PACKAGES/cgdna/examples/oxDNA/ and /oxDNA2/.
 A simple python setup tool which creates single straight or helical DNA strands,
 DNA duplexes or arrays of DNA duplexes can be found in examples/PACKAGES/cgdna/util/.
@@ -128,7 +136,7 @@ Related commands
 :doc:`bond_style oxrna2/fene <bond_oxdna>`, :doc:`pair_coeff <pair_coeff>`,
 :doc:`bond_style oxdna/fene <bond_oxdna>`, :doc:`pair_style oxdna/excv <pair_oxdna>`,
 :doc:`bond_style oxdna2/fene <bond_oxdna>`, :doc:`pair_style oxdna2/excv <pair_oxdna2>`,
-:doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
+:doc:`atom_style oxdna <atom_style>`, :doc:`fix nve/dotc/langevin <fix_nve_dotc_langevin>`
 
 Default
 """""""

doc/utils/sphinx-config/false_positives.txt

@@ -2323,6 +2323,7 @@ Ntriples
 Ntype
 ntypes
 Ntypes
+nucleotide
 nucleotides
 nullptr
 num