Merge pull request lammps#4000 from akohlmey/collected-small-changes

Collected small changes

doc/src/compute_xrd.rst

@@ -62,28 +62,29 @@ equations:
    \frac{\sin(\theta)}{\lambda} &= \frac{\left\lVert\mathbf{k}\right\rVert}{2}
 
 Here, :math:`\mathbf{k}` is the location of the reciprocal lattice node,
-:math:`r_j` is the position of each atom, :math:`f_j` are atomic scattering
-factors, *Lp* is the Lorentz-polarization factor, and :math:`\theta` is the
-scattering angle of diffraction.  The Lorentz-polarization factor can be turned
-off using the optional *LP* keyword.
+:math:`r_j` is the position of each atom, :math:`f_j` are atomic
+scattering factors, *Lp* is the Lorentz-polarization factor, and
+:math:`\theta` is the scattering angle of diffraction.  The
+Lorentz-polarization factor can be turned off using the optional *LP*
+keyword.
 
 Diffraction intensities are calculated on a three-dimensional mesh of
-reciprocal lattice nodes. The mesh spacing is defined either (a) by the entire
-simulation domain or (b) manually using selected values as
-shown in the 2D diagram below.
+reciprocal lattice nodes. The mesh spacing is defined either (a) by the
+entire simulation domain or (b) manually using selected values as shown
+in the 2D diagram below.
 
-.. image:: img/xrd_mesh.jpg
+.. image:: img/xrd_mesh.png
    :scale: 75%
    :align: center
 
 For a mesh defined by the simulation domain, a rectilinear grid is
 constructed with spacing :math:`c A^{-1}` along each reciprocal lattice
-axis, where :math:`A` is a matrix containing the vectors corresponding to the
-edges of the simulation cell. If one or two directions has non-periodic
-boundary conditions, then the spacing in these directions is defined from the
-average of the (inversed) box lengths with periodic boundary conditions.
-Meshes defined by the simulation domain must contain at least one periodic
-boundary.
+axis, where :math:`A` is a matrix containing the vectors corresponding
+to the edges of the simulation cell. If one or two directions has
+non-periodic boundary conditions, then the spacing in these directions
+is defined from the average of the (inversed) box lengths with periodic
+boundary conditions.  Meshes defined by the simulation domain must
+contain at least one periodic boundary.
 
 If the *manual* flag is included, the mesh of reciprocal lattice nodes
 will be defined using the *c* values for the spacing along each

doc/src/fix_adapt.rst

@@ -317,21 +317,21 @@ Currently *bond* does not support bond_style hybrid nor bond_style
 hybrid/overlay as bond styles. The bond styles that currently work
 with fix_adapt are
 
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`class2 <bond_class2>`        | r0         | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`fene <bond_fene>`            | k,r0       | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`fene/nm <bond_fene>`         | k,r0       | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`gromos <bond_gromos>`        | k,r0       | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`harmonic <bond_harmonic>`    | k,r0       | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`morse <bond_morse>`          | r0         | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 | :doc:`nonlinear <bond_nonlinear>`  | epsilon,r0 | type bonds |
-+------------------------------------+-------+-----------------+
++------------------------------------+------------+------------+
 
 ----------
 
@@ -355,11 +355,11 @@ Currently *angle* does not support angle_style hybrid nor angle_style
 hybrid/overlay as angle styles. The angle styles that currently work
 with fix_adapt are
 
-+------------------------------------+-------+-----------------+
-| :doc:`harmonic <angle_harmonic>`    | k,theta0 | type angles |
-+------------------------------------+-------+-----------------+
-| :doc:`cosine <angle_cosine>`        | k        | type angles |
-+------------------------------------+-------+-----------------+
++------------------------------------+----------+-------------+
+| :doc:`harmonic <angle_harmonic>`   | k,theta0 | type angles |
++------------------------------------+----------+-------------+
+| :doc:`cosine <angle_cosine>`       | k        | type angles |
++------------------------------------+----------+-------------+
 
 Note that internally, theta0 is stored in radians, so the variable
 this fix uses to reset theta0 needs to generate values in radians.
@@ -484,7 +484,7 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute ti <compute_ti>`
+:doc:`compute ti <compute_ti>`, :doc:`fix adapt/fep <fix_adapt_fep>`
 
 Default
 """""""

doc/src/pair_beck.rst

@@ -30,11 +30,11 @@ Description
 
 Style *beck* computes interactions based on the potential by
 :ref:`(Beck) <Beck>`, originally designed for simulation of Helium.  It
-includes truncation at a cutoff distance Rc.
+includes truncation at a cutoff distance :math:`r_c`.
 
 .. math::
 
-   E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < R_c \\
+   E(r) &= A \exp\left[-\alpha r - \beta r^6\right] - \frac{B}{\left(r^2+a^2\right)^3} \left(1+\frac{2.709+3a^2}{r^2+a^2}\right) \qquad r < r_c \\
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -50,7 +50,7 @@ commands.
 * cutoff (distance units)
 
 The last coefficient is optional.  If not specified, the global cutoff
-:math:`R_c` is used.
+:math:`r_c` is used.
 
 ----------
 

doc/src/pair_lj_cut_tip4p.rst

@@ -58,6 +58,40 @@ Examples
 Description
 """""""""""
 
+The *lj/cut/tip4p* styles implement the TIP4P water model of
+:ref:`(Jorgensen) <Jorgensen2>` and similar models, which introduce a
+massless site M located a short distance away from the oxygen atom along
+the bisector of the HOH angle.  The atomic types of the oxygen and
+hydrogen atoms, the bond and angle types for OH and HOH interactions,
+and the distance to the massless charge site are specified as pair_style
+arguments and are used to identify the TIP4P-like molecules and
+determine the position of the M site from the positions of the hydrogen
+and oxygen atoms of the water molecules.  The M site location is used
+for all Coulomb interactions instead of the oxygen atom location, also
+with all other atom types, while the location of the oxygen atom is used
+for the Lennard-Jones interactions.  Style *lj/cut/tip4p/cut* uses a
+cutoff for Coulomb interactions; style *lj/cut/tip4p/long* is for use
+with a long-range Coulombic solver (Ewald or PPPM).
+
+.. note::
+
+   For each TIP4P water molecule in your system, the atom IDs for
+   the O and 2 H atoms must be consecutive, with the O atom first.  This
+   is to enable LAMMPS to "find" the 2 H atoms associated with each O
+   atom.  For example, if the atom ID of an O atom in a TIP4P water
+   molecule is 500, then its 2 H atoms must have IDs 501 and 502.
+
+See the :doc:`Howto tip4p <Howto_tip4p>` page for more information
+on how to use the TIP4P pair styles and lists of parameters to set.
+Note that the neighbor list cutoff for Coulomb interactions is
+effectively extended by a distance 2\*qdist when using the TIP4P pair
+style, to account for the offset distance of the fictitious charges on
+O atoms in water molecules.  Thus it is typically best in an
+efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
+shrink the size of the neighbor list.  This leads to slightly larger
+cost for the long-range calculation, so you can test the trade-off for
+your model.
+
 The *lj/cut/tip4p* styles compute the standard 12/6 Lennard-Jones potential,
 given by
 
@@ -91,34 +125,6 @@ specified for this style means that pairwise interactions within this
 distance are computed directly; interactions outside that distance are
 computed in reciprocal space.
 
-The *lj/cut/tip4p* styles implement the TIP4P
-water model of :ref:`(Jorgensen) <Jorgensen2>`, which introduces a massless
-site located a short distance away from the oxygen atom along the
-bisector of the HOH angle.  The atomic types of the oxygen and
-hydrogen atoms, the bond and angle types for OH and HOH interactions,
-and the distance to the massless charge site are specified as
-pair_style arguments.  Style *lj/cut/tip4p/cut* uses a cutoff for
-Coulomb interactions; style *lj/cut/tip4p/long* is for use with a
-long-range Coulombic solver (Ewald or PPPM).
-
-.. note::
-
-   For each TIP4P water molecule in your system, the atom IDs for
-   the O and 2 H atoms must be consecutive, with the O atom first.  This
-   is to enable LAMMPS to "find" the 2 H atoms associated with each O
-   atom.  For example, if the atom ID of an O atom in a TIP4P water
-   molecule is 500, then its 2 H atoms must have IDs 501 and 502.
-
-See the :doc:`Howto tip4p <Howto_tip4p>` page for more information
-on how to use the TIP4P pair styles and lists of parameters to set.
-Note that the neighbor list cutoff for Coulomb interactions is
-effectively extended by a distance 2\*qdist when using the TIP4P pair
-style, to account for the offset distance of the fictitious charges on
-O atoms in water molecules.  Thus it is typically best in an
-efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2\*qdist, to
-shrink the size of the neighbor list.  This leads to slightly larger
-cost for the long-range calculation, so you can test the trade-off for
-your model.
 
 Coefficients
 """"""""""""

doc/src/pair_lj_smooth_linear.rst

@@ -31,13 +31,13 @@ Style *lj/smooth/linear* computes a truncated and force-shifted LJ
 interaction (aka Shifted Force Lennard-Jones) that combines the
 standard 12/6 Lennard-Jones function and subtracts a linear term based
 on the cutoff distance, so that both, the potential and the force, go
-continuously to zero at the cutoff Rc :ref:`(Toxvaerd) <Toxvaerd>`:
+continuously to zero at the cutoff :math:`r_c` :ref:`(Toxvaerd) <Toxvaerd>`:
 
 .. math::
 
    \phi\left(r\right) & =  4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
                        \left(\frac{\sigma}{r}\right)^6 \right] \\
-   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c}       \qquad r < R_c
+   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c}       \qquad r < r_c
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -77,8 +77,9 @@ tail option for adding long-range tail corrections to energy and
 pressure, since the energy of the pair interaction is smoothed to 0.0
 at the cutoff.
 
-This pair style writes its information to :doc:`binary restart files <restart>`, 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 writes its information to :doc:`binary restart files <restart>`,
+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
 :doc:`run_style respa <run_style>` command.  It does not support the

doc/src/pair_mie.rst

@@ -35,7 +35,7 @@ The *mie/cut* style computes the Mie potential, given by
    E =  C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
                          \qquad r < r_c
 
-Rc is the cutoff and C is a function that depends on the repulsive and
+:math:`r_c` is the cutoff and C is a function that depends on the repulsive and
 attractive exponents, given by:
 
 .. math::

doc/src/pair_morse.rst

@@ -53,7 +53,7 @@ Style *morse* computes pairwise interactions with the formula
    E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
        \qquad r < r_c
 
-Rc is the cutoff.
+:math:`r_c` is the cutoff.
 
 The following coefficients must be defined for each pair of atoms
 types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
@@ -78,7 +78,7 @@ so that both, potential energy and force, go to zero at the cut-off:
 .. math::
 
    \phi\left(r\right) & =  D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c \\
-   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c}       \qquad r < R_c
+   E\left(r\right) & =  \phi\left(r\right)  - \phi\left(r_c\right) - \left(r - r_c\right) \left.\frac{d\phi}{d r} \right|_{r=r_c}       \qquad r < r_c
 
 The syntax of the pair_style and pair_coeff commands are the same for
 the *morse* and *morse/smooth/linear* styles.

doc/src/pair_soft.rst

@@ -44,8 +44,9 @@ It is useful for pushing apart overlapping atoms, since it does not
 blow up as r goes to 0.  A is a prefactor that can be made to vary in
 time from the start to the end of the run (see discussion below),
 e.g. to start with a very soft potential and slowly harden the
-interactions over time.  Rc is the cutoff.  See the :doc:`fix nve/limit <fix_nve_limit>` command for another way to push apart
-overlapping atoms.
+interactions over time.  :math:`r_c` is the cutoff.
+See the :doc:`fix nve/limit <fix_nve_limit>` command for another way
+to push apart overlapping atoms.
 
 The following coefficients must be defined for each pair of atom types
 via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,

doc/src/pair_spica.rst

@@ -81,7 +81,7 @@ given by
 
 as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
 :ref:`(Shinoda) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
-Rc is the cutoff.
+:math:`r_c` is the cutoff.
 Summary information on these force fields can be found at https://www.spica-ff.org
 
 Style *lj/spica/coul/long* computes the adds Coulombic interactions

examples/PACKAGES/phonon/2-1D-diatomic/in.Ana

@@ -2,15 +2,15 @@
 dimension   2
 boundary    p f p
 
-units		   lj
-atom_style	bond
+units              lj
+atom_style      bond
 atom_modify sort 0 1.
 bond_style  harmonic
 pair_style  none
-communicate single cutoff 2.0
+comm_modify cutoff 2.0
 
 # geometry
-read_data	data.pos
+read_data       data.pos
 
 #
 neighbor 1.0 nsq
@@ -43,4 +43,4 @@ thermo_modify temp MyTemp
 thermo   100
 
 #
-run 		 2000000
+run              2000000

src/MDI/fix_mdi_engine.cpp

@@ -28,7 +28,8 @@ using namespace FixConst;
 
 /* ---------------------------------------------------------------------- */
 
-FixMDIEngine::FixMDIEngine(LAMMPS *_lmp, int narg, char **arg) : Fix(_lmp, narg, arg)
+FixMDIEngine::FixMDIEngine(LAMMPS *_lmp, int narg, char **arg) :
+    Fix(_lmp, narg, arg), mdi_engine(nullptr)
 {
   if (narg != 3) error->all(FLERR, "Illegal fix mdi/engine command");
 }

src/MDI/fix_mdi_qm.cpp

@@ -35,7 +35,10 @@ static int compare_IDs(const int, const int, void *);
 
 /* ---------------------------------------------------------------------- */
 
-FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) :
+    Fix(lmp, narg, arg), id_mcfix(nullptr), mc_active_ptr(nullptr), exclusion_group_ptr(nullptr),
+    elements(nullptr), qmIDs(nullptr), qm2owned(nullptr), eqm(nullptr), eqm_mine(nullptr),
+    tqm(nullptr), tqm_mine(nullptr), xqm(nullptr), xqm_mine(nullptr), fqm(nullptr)
 {
   // check requirements for LAMMPS to work with MDI as an engine
   // atom IDs do not need to be consecutive
@@ -58,9 +61,7 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
   addflag = 1;
   every = 1;
   connectflag = 1;
-  elements = nullptr;
   mcflag = 0;
-  id_mcfix = nullptr;
 
   int iarg = 3;
   while (iarg < narg) {
@@ -178,18 +179,6 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
   nqm = nqm_last = max_nqm = 0;
   nexclude = 0;
 
-  qmIDs = nullptr;
-  qm2owned = nullptr;
-
-  eqm = nullptr;
-  tqm = nullptr;
-  xqm = nullptr;
-  fqm = nullptr;
-
-  eqm_mine = nullptr;
-  tqm_mine = nullptr;
-  xqm_mine = nullptr;
-
   // per-atom data
 
   nmax = atom->nmax;
@@ -999,9 +988,8 @@ void FixMDIQM::send_box()
     ierr = MDI_Send(qm_cell, 9, MDI_DOUBLE, mdicomm);
     if (ierr) error->all(FLERR, "MDI: >CELL data");
 
-  } else if (domain->xperiodic == 1 || domain->yperiodic == 1 ||
-             domain->zperiodic == 1) {
-    error->all(FLERR,"MDI requires fully periodic or fully non-periodic system");
+  } else if (domain->xperiodic == 1 || domain->yperiodic == 1 || domain->zperiodic == 1) {
+    error->all(FLERR, "MDI requires fully periodic or fully non-periodic system");
   }
 }
 

src/MDI/fix_mdi_qmmm.cpp

@@ -39,7 +39,11 @@ static int compare_IDs(const int, const int, void *);
 
 /* ---------------------------------------------------------------------- */
 
-FixMDIQMMM::FixMDIQMMM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
+FixMDIQMMM::FixMDIQMMM(LAMMPS *lmp, int narg, char **arg) :
+    Fix(lmp, narg, arg), elements(nullptr), pair_coul(nullptr), qmIDs(nullptr), qm2owned(nullptr),
+    eqm(nullptr), eqm_mine(nullptr), tqm(nullptr), tqm_mine(nullptr), xqm(nullptr),
+    xqm_mine(nullptr), qqm(nullptr), qqm_mine(nullptr), qpotential(nullptr),
+    qpotential_mine(nullptr), fqm(nullptr), ecoul(nullptr)
 {
   // check requirements for LAMMPS to work with MDI for a QMMM engine
   // atom IDs do not need to be consecutive
@@ -69,7 +73,6 @@ FixMDIQMMM::FixMDIQMMM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
 
   virialflag = 0;
   connectflag = 1;
-  elements = nullptr;
 
   int iarg = 4;
   while (iarg < narg) {
@@ -1782,9 +1785,8 @@ void FixMDIQMMM::send_box()
     ierr = MDI_Send(qm_cell, 9, MDI_DOUBLE, mdicomm);
     if (ierr) error->all(FLERR, "MDI: >CELL data");
 
-  } else if (domain->xperiodic == 1 || domain->yperiodic == 1 ||
-             domain->zperiodic == 1) {
-    error->all(FLERR,"MDI requires fully periodic or fully non-periodic system");
+  } else if (domain->xperiodic == 1 || domain->yperiodic == 1 || domain->zperiodic == 1) {
+    error->all(FLERR, "MDI requires fully periodic or fully non-periodic system");
   }
 }