Merge pull request #2010 from akohlmey/collected-small-fixes

src/KOKKOS/pair_vashishta_kokkos.*  @andeplane

src/MANYBODY/pair_vashishta_table.* @andeplane

src/MANYBODY/pair_atm.*             @sergeylishchuk

src/USER-MISC/fix_bond_react.*      @jrgissing

src/USER-REACTION/fix_bond_react.*  @jrgissing

src/USER-MISC/*_grem.*              @dstelter92

src/USER-MISC/compute_stress_mop*.* @RomainVermorel

For headers declaring functions of the C-library, the corresponding

C++ versions should be included (examples: `#include <cstdlib>` or

`#include <cctypes>`).  However, these includes are limited to those defined

in the C++98 standard.  Some files thus must use the older style until

the minimum C++ standard requirement of LAMMPS is lifted to C++11 or

even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`

or `#include <inttypes.h>` versus `#include <cinttypes>`).

`#include <cctypes>` instead of `#include <stdlib.h>` or

`#include<ctypes.h>` ).

### C++ Standard Compliance

LAMMPS core files currently correspond to the C++98 standard. Files

requiring C++11 or later are only permitted in (optional) packages

and particularly packages that are not part of the list of commonly

used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.

Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.

Since using both at the same time can cause problems, iostreams should

be avoided where possible.

LAMMPS core files use standard conforming C++ compatible with the

C++11 standard, unless explicitly noted.  Also, LAMMPS uses the C-style

stdio library for I/O instead of iostreams.  Since using both at the

same time can cause problems, iostreams should be avoided where possible.

### Lean Header Files

compute stress/atom command

===========================

compute centroid/stress/atom command

====================================

Restrictions

""""""""""""

Currently, compute *centroid/stress/atom* does not support

pair styles with many-body interactions,

such as :doc:`Tersoff <pair_tersoff>`,

and LAMMPS will generate an error in such cases.

In principal, equivalent formulation

to that of angle, dihedral and improper contributions

in the virial :math:`W_{ab}` formula

can also be applied to the many-body pair styles,

and is planned in the future.

Currently (Spring 2020), compute *centroid/stress/atom* does not support

pair styles with many-body interactions, such as :doc:`Tersoff

<pair_tersoff>`, or pair styles with long-range Coulomb interactions.

LAMMPS will generate an error in such cases.  In principal, equivalent

formulation to that of angle, dihedral and improper contributions in the

virial :math:`W_{ab}` formula can also be applied to the many-body pair

styles, and is planned in the future.

Related commands

""""""""""""""""

energy added or subtracted to it.  If not specified, then the atoms in

the group are affected wherever they may move to.

Heat addition/subtraction is performed every N timesteps.  The *eflux*

parameter can be specified as a numeric constant or as a variable (see

below).  If it is a numeric constant or equal-style variable which

evaluates to a scalar value, then the *eflux* determines the change in

aggregate energy of the entire group of atoms per unit time, e.g. in

eV/psec for :doc:`metal units <units>`.  In this case it is an

"extensive" quantity, meaning its magnitude should be scaled with the

number of atoms in the group.  Note that since *eflux* has per-time

units (i.e. it is a flux), this means that a larger value of N will

add/subtract a larger amount of energy each time the fix is invoked.

Heat addition/subtraction is performed every N timesteps.

The *eflux* parameter can be specified as a numeric constant or as an

equal- or atom-style :doc:`variable <variable>`.  If the value is a

variable, it should be specified as v_name, where *name* is the variable

name.  In this case, the variable will be evaluated each timestep, and

its current value(s) used to determine the flux.

If *eflux* is a numeric constant or equal-style variable which evaluates

to a scalar value, then *eflux* determines the change in aggregate energy

of the entire group of atoms per unit time, e.g. in eV/psec for

:doc:`metal units <units>`.  In this case it is an "extensive" quantity,

meaning its magnitude should be scaled with the number of atoms in the

group.  Note that since *eflux* also has per-time units (i.e. it is a

flux), this means that a larger value of N will add/subtract a larger

amount of energy each time the fix is invoked.

.. note::

time.  In this case, each value is an "intensive" quantity, which need

not be scaled with the number of atoms in the group.

As mentioned above, the *eflux* parameter can be specified as an

equal-style or atom_style :doc:`variable <variable>`.  If the value is a

variable, it should be specified as v_name, where name is the variable

name.  In this case, the variable will be evaluated each timestep, and

its value(s) used to determine the flux.

Equal-style variables can specify formulas with various mathematical

functions, and include :doc:`thermo_style <thermo_style>` command

keywords for the simulation box parameters and timestep and elapsed

void PairBuckLongCoulLong::write_data_all(FILE *fp)

{

  for (int i = 1; i <= atom->ntypes; i++)

    for (int j = i; j <= atom->ntypes; j++)

  for (int i = 1; i <= atom->ntypes; i++) {

    for (int j = i; j <= atom->ntypes; j++) {

      if (ewald_order & (1<<6)) {

      fprintf(fp,"%d %d %g %g\n",i,j,

              buck_a_read[i][j],buck_rho_read[i][j]);

      } else {

        fprintf(fp,"%d %d %g %g %g\n",i,j,

                buck_a_read[i][j],buck_rho_read[i][j],buck_c_read[i][j]);

      }

    }

  }

}

/* ----------------------------------------------------------------------

   compute pair interactions