Merge branch 'develop' into distributed-grids

.github/CODEOWNERS

@@ -64,6 +64,8 @@ src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/REPLICA/*_grem.*                @dstelter92
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
 src/MISC/*_tracker.*                @jtclemm
+src/MC/fix_gcmc.*                   @athomps
+src/MC/fix_sgcmc.*                  @athomps
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp

cmake/CMakeLists.txt

@@ -668,7 +668,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()

cmake/Modules/Packages/MC.cmake

@@ -0,0 +1,9 @@
+# fix sgcmc may only be installed if also the EAM pair style from MANYBODY is installed
+if(NOT PKG_MANYBODY)
+  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
+  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.h)
+  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()

doc/src/Build_extras.rst

@@ -36,6 +36,7 @@ This is the list of packages that may require additional steps.
    * :ref:`AWPMD <awpmd>`
    * :ref:`COLVARS <colvars>`
    * :ref:`COMPRESS <compress>`
+   * :ref:`ELECTRODE <electrode>`
    * :ref:`GPU <gpu>`
    * :ref:`H5MD <h5md>`
    * :ref:`INTEL <intel>`

doc/src/Commands_fix.rst

@@ -214,6 +214,7 @@ OPT.
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
    * :doc:`setforce/spin <fix_setforce>`
+   * :doc:`sgcmc <fix_sgcmc>`
    * :doc:`shake (k) <fix_shake>`
    * :doc:`shardlow (k) <fix_shardlow>`
    * :doc:`smd <fix_smd>`

doc/src/Commands_removed.rst

@@ -11,6 +11,8 @@ with the direct alternative (if available) and print a warning.
 Fix ave/spatial and fix ave/spatial/sphere
 ------------------------------------------
 
+.. deprecated:: 11Dec2015
+
 The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
 since they were superseded by the more general and extensible "chunk
 infrastructure".  Here the system is partitioned in one of many possible

doc/src/Packages_details.rst

@@ -1486,8 +1486,9 @@ MC package
 
 Several fixes and a pair style that have Monte Carlo (MC) or MC-like
 attributes.  These include fixes for creating, breaking, and swapping
-bonds, for performing atomic swaps, and performing grand-canonical MC
+bonds, for performing atomic swaps, and performing grand canonical
-(GCMC) or similar processes in conjunction with dynamics.
+MC (GCMC), semi-grand canonical MC (SGCMC), or similar processes in
+conjunction with molecular dynamics (MD).
 
 **Supporting info:**
 
@@ -1499,6 +1500,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
 * :doc:`fix bond/swap <fix_bond_swap>`
 * :doc:`fix charge/regulation <fix_charge_regulation>`
 * :doc:`fix gcmc <fix_gcmc>`
+* :doc:`fix sgcmc <fix_sgcmc>`
 * :doc:`fix tfmc <fix_tfmc>`
 * :doc:`fix widom <fix_widom>`
 * :doc:`pair_style dsmc <pair_dsmc>`

doc/src/fix.rst

@@ -366,6 +366,7 @@ accelerated styles exist.
 * :doc:`saed/vtk <fix_saed_vtk>` - time-average the intensities from :doc:`compute saed <compute_saed>`
 * :doc:`setforce <fix_setforce>` - set the force on each atom
 * :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
+* :doc:`sgcmc <fix_sgcmc>` - fix for hybrid semi-grand canonical MD/MC simulations
 * :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
 * :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting
 * :doc:`smd <fix_smd>` - applied a steered MD force to a group

doc/src/fix_ave_spatial.rst

@@ -0,0 +1,9 @@
+Fix ave/spatial command
+=======================
+
+.. meta::
+   :http-equiv=Refresh: 5; url='https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere'
+
+.. deprecated:: 11Dec2015
+
+The `fix ave/spatial` command has been superseded by :doc:`fix ave/chunk <fix_ave_chunk>`.

doc/src/fix_ave_spatial_sphere.rst

@@ -0,0 +1,9 @@
+Fix ave/spatial command
+=======================
+
+.. meta::
+   :http-equiv=Refresh: 5; url='https://docs.lammps.org/Commands_removed.html#fix-ave-spatial-and-fix-ave-spatial-sphere'
+
+.. deprecated:: 11Dec2015
+
+The `fix ave/spatial/sphere` command has been superseded by :doc:`fix ave/chunk <fix_ave_chunk>`.

doc/src/fix_sgcmc.rst

@@ -0,0 +1,188 @@
+.. index:: fix sgcmc
+
+fix sgcmc command
+=================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID sgcmc every_nsteps swap_fraction temperature deltamu ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* sgcmc = style name of this fix command
+* every_nsteps = number of MD steps between MC cycles
+* swap_fraction = fraction of a full MC cycle carried out at each call (a value of 1.0 will perform as many trial moves as there are atoms)
+* temperature = temperature that enters Boltzmann factor in Metropolis criterion (usually the same as MD temperature)
+* deltamu = chemical potential difference(s) (`N-1` values must be provided, with `N` being the number of elements)
+* Zero or more keyword/value pairs may be appended to fix definition line:
+
+  .. parsed-literal::
+
+     keyword = *variance* or *randseed* or *window_moves* or *window_size*
+       *variance* kappa conc1 [conc2] ... [concN]
+         kappa = variance constraint parameter
+         conc1,conc2,...  = target concentration(s) in the range 0.0-1.0 (*N-1* values must be provided, with *N* being the number of elements)
+       *randseed* N
+         N = seed for pseudo random number generator
+       *window_moves* N
+         N = number of times sampling window is moved during one MC cycle
+       *window_size* frac
+         frac = size of sampling window (must be between 0.5 and 1.0)
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix mc all sgcmc 50 0.1 400.0 -0.55
+   fix vc all sgcmc 20 0.2 700.0 -0.7 randseed 324234 variance 2000.0 0.05
+   fix 2  all sgcmc 20 0.1 700.0 -0.7 window_moves 20
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+This command allows to carry out parallel hybrid molecular
+dynamics/Monte Carlo (MD/MC) simulations using the algorithms described
+in :ref:`(Sadigh1) <Sadigh1>`.  Simulations can be carried out in either
+the semi-grand canonical (SGC) or variance constrained semi-grand
+canonical (VC-SGC) ensemble :ref:`(Sadigh2) <Sadigh2>`. Only atom type
+swaps are performed by the SGCMC fix. Relaxations are accounted for by
+the molecular dynamics integration steps.
+
+This fix can be used with standard multi-element EAM potentials
+(:doc:`pair styles eam/alloy or eam/fs <pair_eam>`)
+
+The SGCMC fix can handle Finnis/Sinclair type EAM potentials where
+:math:`\rho(r)` is atom-type specific, such that different elements can
+contribute differently to the total electron density at an atomic site
+depending on the identity of the element at that atomic site.
+
+------------
+
+If this fix is applied, the regular MD simulation will be interrupted in
+defined intervals to carry out a fraction of a Monte Carlo (MC)
+cycle. The interval is set using the parameter *every_nsteps* which
+determines how many MD integrator steps are taken between subsequent
+calls to the MC routine.
+
+It is possible to carry out pure lattice MC simulations by setting
+*every_nsteps* to 1 and not defining an integration fix such as NVE,
+NPT etc.  In that case, the particles will not move and only the MC
+routine will be called to perform atom type swaps.
+
+The parameter *swap_fraction* determines how many MC trial steps are carried
+out every time the MC routine is entered. It is measured in units of full MC
+cycles where one full cycle, *swap_fraction=1*, corresponds to as many MC
+trial steps as there are atoms.
+
+------------
+
+The parameter *temperature* specifies the temperature that is used
+to evaluate the Metropolis acceptance criterion. While it usually
+should be set to the same value as the MD temperature there are cases
+when it can be useful to use two different values for at least part of
+the simulation, e.g., to speed up equilibration at low temperatures.
+
+------------
+
+The parameter *deltamu* is used to set the chemical potential difference
+in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 <Sadigh1>`). By
+convention it is the difference of the chemical potentials of elements
+`B`, `C` ..., with respect to element A. When the simulation includes
+`N` elements, `N-1` values must be specified.
+
+------------
+
+The variance-constrained SGC MC algorithm is activated if the keyword
+*variance* is used. In that case the fix parameter *deltamu* determines
+the effective average constraint in the parallel VC-SGC MC algorithm
+(parameter :math:`\delta\mu_0` in Eq. (20) of :ref:`Sadigh1
+<Sadigh1>`). The parameter *kappa* specifies the variance constraint
+(see Eqs. (20-21) in :ref:`Sadigh1 <Sadigh1>`).
+
+The parameter *conc* sets the target concentration (parameter
+:math:`c_0` in Eqs.  (20-21) of :ref:`Sadigh1 <Sadigh1>`). The atomic
+concentrations refer to components `B`, `C` ..., with `A` being set
+automatically. When the simulation includes `N` elements, `N-1`
+concentration values must be specified.
+
+------------
+
+There are several technical parameters that can be set via optional flags.
+
+*randseed* is expected to be a positive integer number and is used
+to initialize the random number generator on each processor.
+
+*window_size* controls the size of the sampling window in a parallel MC
+simulation. The size has to lie between 0.5 and 1.0. Normally, this
+parameter should be left unspecified which instructs the code to choose
+the optimal window size automatically (see Sect. III.B and Figure 6 in
+:ref:`Sadigh1 <Sadigh1>` for details).
+
+The number of times the window is moved during a MC cycle is set using
+the parameter *window_moves* (see Sect. III.B in :ref:`Sadigh1
+<Sadigh1>` for details).
+
+------------
+
+Restart, fix_modify, output, run start/stop, minimize info
+==========================================================
+
+No information about this fix is written to restart files.
+
+The MC routine keeps track of the global concentration(s) as well as the
+number of accepted and rejected trial swaps during each MC step. These
+values are provided by the sgcmc fix in the form of a global vector that
+can be accessed by various :doc:`output commands <Howto_output>`
+components of the vector represent the following quantities:
+
+* 1 = The absolute number of accepted trial swaps during the last MC step
+* 2 = The absolute number of rejected trial swaps during the last MC step
+* 3 = The current global concentration of species *A* (= number of atoms of type 1 / total number of atoms)
+* 4 = The current global concentration of species *B* (= number of atoms of type 2 / total number of atoms)
+* ...
+* N+2: The current global concentration of species *X* (= number of atoms of type *N* / total number of atoms)
+
+Restrictions
+============
+
+This fix is part of the MC package. It is only enabled if LAMMPS was
+built with that package.  See the :doc:`Build package <Build_package>`
+page for more info.
+
+At present the fix provides optimized subroutines for EAM type
+potentials (see above) that calculate potential energy changes due to
+*local* atom type swaps very efficiently.  Other potentials are
+supported by using the generic potential functions. This, however, will
+lead to exceedingly slow simulations since it implies that the
+energy of the *entire* system is recomputed at each MC trial step.  If
+other potentials are to be used it is strongly recommended to modify and
+optimize the existing generic potential functions for this purpose.
+Also, the generic energy calculation can not be used for parallel
+execution i.e. it only works with a single MPI process.
+
+------------
+
+Default
+=======
+
+The optional parameters default to the following values:
+
+* *randseed* = 324234
+* *window_moves* = 8
+* *window_size* = automatic
+
+------------
+
+.. _Sadigh1:
+
+**(Sadigh1)** B. Sadigh, P. Erhart, A. Stukowski, A. Caro, E. Martinez, and L. Zepeda-Ruiz, Phys. Rev. B **85**, 184203 (2012)
+
+.. _Sadigh2:
+
+**(Sadigh2)** B. Sadigh and P. Erhart, Phys. Rev. B **86**, 134204 (2012)

doc/src/pair_coul.rst

@@ -174,11 +174,11 @@ shifted force model described in :ref:`Fennell <Fennell1>`, given by:
    E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} -  \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
    \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} +  \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2    r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
 
-where :math:`\alpha` is the damping parameter and erfc() is the
+where :math:`\alpha` is the damping parameter and *erfc()* is the
-complementary error-function. The potential corrects issues in the
+complementary error-function. The potential corrects issues in the Wolf
-Wolf model (described below) to provide consistent forces and energies
+model (described below) to provide consistent forces and energies (the
-(the Wolf potential is not differentiable at the cutoff) and smooth
+Wolf potential is not differentiable at the cutoff) and smooth decay to
-decay to zero.
+zero.
 
 ----------
 
@@ -192,30 +192,32 @@ summation method, described in :ref:`Wolf <Wolf1>`, given by:
    \frac{1}{2} \sum_{j \neq i}
    \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
-where :math:`\alpha` is the damping parameter, and erc() and erfc() are
+where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()*
-error-function and complementary error-function terms.  This potential
+are error-function and complementary error-function terms.  This
-is essentially a short-range, spherically-truncated,
+potential is essentially a short-range, spherically-truncated,
 charge-neutralized, shifted, pairwise *1/r* summation.  With a
 manipulation of adding and subtracting a self term (for i = j) to the
-first and second term on the right-hand-side, respectively, and a
+first and second term on the right-hand-side, respectively, and a small
-small enough :math:`\alpha` damping parameter, the second term shrinks and
+enough :math:`\alpha` damping parameter, the second term shrinks and the
-the potential becomes a rapidly-converging real-space summation.  With
+potential becomes a rapidly-converging real-space summation.  With a
-a long enough cutoff and small enough :math:`\alpha` parameter, the energy and
+long enough cutoff and small enough :math:`\alpha` parameter, the energy
-forces calculated by the Wolf summation method approach those of the
+and forces calculated by the Wolf summation method approach those of the
 Ewald sum.  So it is a means of getting effective long-range
 interactions with a short-range potential.
 
 ----------
 
-Style *coul/streitz* is the Coulomb pair interaction defined as part
+Style *coul/streitz* is the Coulomb pair interaction defined as part of
-of the Streitz-Mintmire potential, as described in :ref:`this paper <Streitz2>`, in which charge distribution about an atom is modeled
+the Streitz-Mintmire potential, as described in :ref:`this paper
-as a Slater 1\ *s* orbital.  More details can be found in the referenced
+<Streitz2>`, in which charge distribution about an atom is modeled as a
+Slater 1\ *s* orbital.  More details can be found in the referenced
 paper.  To fully reproduce the published Streitz-Mintmire potential,
-which is a variable charge potential, style *coul/streitz* must be
+which is a variable charge potential, style *coul/streitz* must be used
-used with :doc:`pair_style eam/alloy <pair_eam>` (or some other
+with :doc:`pair_style eam/alloy <pair_eam>` (or some other short-range
-short-range potential that has been parameterized appropriately) via
+potential that has been parameterized appropriately) via the
-the :doc:`pair_style hybrid/overlay <pair_hybrid>` command.  Likewise,
+:doc:`pair_style hybrid/overlay <pair_hybrid>` command.  Likewise,
-charge equilibration must be performed via the :doc:`fix qeq/slater <fix_qeq>` command. For example:
+charge equilibration must be performed via the :doc:`fix qeq/slater
+<fix_qeq>` command. For example:
 
 .. code-block:: LAMMPS
 

doc/src/pair_tracker.rst

@@ -174,8 +174,8 @@ the specified attribute.
 Restrictions
 """"""""""""
 
-This fix is part of the MISC package.  It is only enabled if LAMMPS
+This pair style is part of the MISC package.  It is only enabled if
-was built with that package.  See the :doc:`Build package
+LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
 This pair style is currently incompatible with granular pair styles

doc/utils/sphinx-config/false_positives.txt

@@ -696,6 +696,7 @@ delocalized
 Delong
 delr
 deltaHf
+deltamu
 dem
 Dendrimer
 dendritic
@@ -985,7 +986,6 @@ equilization
 equipartitioning
 eradius
 erate
-erc
 Ercolessi
 Erdmann
 erf
@@ -2513,6 +2513,7 @@ Nstart
 nstats
 Nstep
 Nsteps
+nsteps
 nsteplast
 Nstop
 nsub
@@ -3233,6 +3234,7 @@ setvel
 sfftw
 sfree
 Sg
+sgcmc
 Shan
 Shanno
 Shapeev

examples/mc/in.sgcmc.eam

@@ -0,0 +1,48 @@
+# general variables
+variable        temperature equal 700
+variable        size equal 20
+
+# variables for 'fix sgcmc'
+variable        nsteps_mc     equal 100
+variable        swap_fraction equal 0.2
+variable        temperature_mc equal ${temperature}
+variable        deltamu equal -0.70
+variable        target_concentration equal 0.02
+variable        kappa equal 1e3
+
+# general settings
+units           metal
+atom_style      atomic
+
+# set up structure
+boundary        p p p
+lattice         bcc 2.88
+region          box block 0 ${size}  0 ${size}  0 ${size}
+create_box      2 box
+create_atoms    1 box
+reset_timestep  0
+timestep        0.0025
+
+# set up interaction
+pair_style      eam/fs
+pair_coeff      * * FeCu.pasianot.eamfs Fe Cu
+
+# initialize velocities
+variable        double_temp equal ${temperature}*2
+velocity        all create ${double_temp} 428459 dist gaussian
+
+# what and how to run
+fix             integrate all npt &
+                temp ${temperature} ${temperature} 1.7 &
+                aniso 0.0 0.0 1.5
+fix             mc all sgcmc ${nsteps_mc} ${swap_fraction} ${temperature_mc} ${deltamu} &
+                randseed 324234 &
+                variance ${kappa} ${target_concentration}
+
+# set up output
+thermo          100
+thermo_style    custom step temp atoms pe press &
+                lx ly lz f_mc[1] f_mc[2] f_mc[3] f_mc[4]
+#dump            1 all custom 200 mc.*.dump id type x y z
+
+run             2000

examples/mc/log.13Dec22.sgcmc.eam.g++.1

@@ -0,0 +1,143 @@
+LAMMPS (3 Nov 2022)
+  using 1 OpenMP thread(s) per MPI task
+# general variables
+variable        temperature equal 700
+variable        size equal 20
+
+# variables for 'fix sgcmc'
+variable        nsteps_mc     equal 100
+variable        swap_fraction equal 0.2
+variable        temperature_mc equal ${temperature}
+variable        temperature_mc equal 700
+variable        deltamu equal -0.70
+variable        target_concentration equal 0.02
+variable        kappa equal 1e3
+
+# general settings
+units           metal
+atom_style      atomic
+
+# set up structure
+boundary        p p p
+lattice         bcc 2.88
+Lattice spacing in x,y,z = 2.88 2.88 2.88
+region          box block 0 ${size}  0 ${size}  0 ${size}
+region          box block 0 20  0 ${size}  0 ${size}
+region          box block 0 20  0 20  0 ${size}
+region          box block 0 20  0 20  0 20
+create_box      2 box
+Created orthogonal box = (0 0 0) to (57.6 57.6 57.6)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 16000 atoms
+  using lattice units in orthogonal box = (0 0 0) to (57.6 57.6 57.6)
+  create_atoms CPU = 0.001 seconds
+reset_timestep  0
+timestep        0.0025
+
+# set up interaction
+pair_style      eam/fs
+pair_coeff      * * FeCu.pasianot.eamfs Fe Cu
+
+# initialize velocities
+variable        double_temp equal ${temperature}*2
+variable        double_temp equal 700*2
+velocity        all create ${double_temp} 428459 dist gaussian
+velocity        all create 1400 428459 dist gaussian
+
+# what and how to run
+fix             integrate all npt                 temp ${temperature} ${temperature} 1.7                 aniso 0.0 0.0 1.5
+fix             integrate all npt                 temp 700 ${temperature} 1.7                 aniso 0.0 0.0 1.5
+fix             integrate all npt                 temp 700 700 1.7                 aniso 0.0 0.0 1.5
+fix             mc all sgcmc ${nsteps_mc} ${swap_fraction} ${temperature_mc} ${deltamu}                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 ${swap_fraction} ${temperature_mc} ${deltamu}                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 0.2 ${temperature_mc} ${deltamu}                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 0.2 700 ${deltamu}                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 0.2 700 -0.7                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 0.2 700 -0.7                 randseed 324234                 variance 1000 ${target_concentration}
+fix             mc all sgcmc 100 0.2 700 -0.7                 randseed 324234                 variance 1000 0.02
+  SGC - Number of MD timesteps: 100
+  SGC - Fraction of swap atoms: 0.2
+  SGC - Temperature: %f
+  SGC - Chemical potential of species 2: -0.7
+  SGC - Random number seed: 324234
+  SGC - Kappa: 1000
+  SGC - Target concentration of species 2: 0.02
+  SGC - Target concentration of species 1: 0.98
+
+# set up output
+thermo          100
+thermo_style    custom step temp atoms pe press                 lx ly lz f_mc[1] f_mc[2] f_mc[3] f_mc[4]
+#dump            1 all custom 200 mc.*.dump id type x y z
+
+run             2000
+  SGC - Interaction radius: 5.50679
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.50679
+  ghost atom cutoff = 7.50679
+  binsize = 3.753395, bins = 16 16 16
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/fs, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) fix sgcmc, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 25.06 | 25.06 | 25.06 Mbytes
+   Step          Temp         Atoms        PotEng         Press            Lx             Ly             Lz          f_mc[1]        f_mc[2]        f_mc[3]        f_mc[4]    
+         0   1400               16000  -65889.786     -28854.541      57.6           57.6           57.6           0              0              1              0            
+       100   734.32713          16000  -64514.143      5439.4277      57.327173      57.322333      57.318848      12             3188           0.99925        0.00075      
+       200   678.63428          16000  -64386.224     -920.7819       57.423954      57.409111      57.412727      22             3178           0.997875       0.002125     
+       300   683.24749          16000  -64370.598     -1609.0429      57.427441      57.424568      57.426831      20             3180           0.996625       0.003375     
+       400   689.28007          16000  -64359.115      2489.3933      57.376537      57.379856      57.372895      27             3173           0.9949375      0.0050625    
+       500   693.85333          16000  -64337.222     -1935.9815      57.435754      57.43493       57.427453      18             3182           0.9938125      0.0061875    
+       600   693.52855          16000  -64314.465      380.8264       57.410314      57.397604      57.408337      21             3179           0.9925         0.0075       
+       700   690.62721          16000  -64284.369      208.21986      57.412407      57.407285      57.410684      31             3169           0.9905625      0.0094375    
+       800   687.08129          16000  -64244.443     -936.31731      57.425765      57.438983      57.421321      31             3169           0.988625       0.011375     
+       900   696.07347          16000  -64230.523      932.65537      57.414588      57.413865      57.402817      27             3173           0.9869375      0.0130625    
+      1000   691.70667          16000  -64194.151     -690.02055      57.429033      57.420053      57.443245      23             3177           0.9855         0.0145       
+      1100   691.21797          16000  -64169.016     -86.623524      57.42147       57.424262      57.436841      35             3165           0.9833125      0.0166875    
+      1200   691.27155          16000  -64134.443      411.68129      57.425111      57.432481      57.4118        42             3158           0.9806875      0.0193125    
+      1300   693.76194          16000  -64098.615     -943.9013       57.446704      57.448382      57.440727      64             3136           0.9800625      0.0199375    
+      1400   691.16411          16000  -64080.423      1248.7921      57.417118      57.409651      57.435099      104            3096           0.9799375      0.0200625    
+      1500   694.49681          16000  -64084.428     -179.5269       57.440533      57.432581      57.434409      68             3132           0.9799375      0.0200625    
+      1600   697.58329          16000  -64089.682     -761.14401      57.450616      57.450654      57.422293      97             3103           0.98           0.02         
+      1700   697.57549          16000  -64090.2        1370.3938      57.399319      57.423969      57.426788      85             3115           0.9801875      0.0198125    
+      1800   694.18435          16000  -64083.812     -1381.5398      57.446114      57.438096      57.475109      84             3116           0.9799375      0.0200625    
+      1900   702.82577          16000  -64096.005      918.83968      57.452789      57.404638      57.408161      70             3130           0.9799375      0.0200625    
+      2000   696.02963          16000  -64080.059      276.99031      57.443085      57.452012      57.403928      81             3119           0.980125       0.019875     
+Loop time of 48.793 on 1 procs for 2000 steps with 16000 atoms
+
+Performance: 8.854 ns/day, 2.711 hours/ns, 40.989 timesteps/s, 655.831 katom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 47.46      | 47.46      | 47.46      |   0.0 | 97.27
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.13269    | 0.13269    | 0.13269    |   0.0 |  0.27
+Output  | 0.0011432  | 0.0011432  | 0.0011432  |   0.0 |  0.00
+Modify  | 1.0996     | 1.0996     | 1.0996     |   0.0 |  2.25
+Other   |            | 0.0993     |            |       |  0.20
+
+Nlocal:          16000 ave       16000 max       16000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          17201 ave       17201 max       17201 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:      1.344e+06 ave   1.344e+06 max   1.344e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:    2.688e+06 ave   2.688e+06 max   2.688e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2688000
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:48

examples/mc/log.13Dec22.sgcmc.eam.g++.4

@@ -0,0 +1,143 @@
+LAMMPS (3 Nov 2022)
+  using 1 OpenMP thread(s) per MPI task
+# general variables
+variable        temperature equal 700
+variable        size equal 20
+
+# variables for 'fix sgcmc'
+variable        nsteps_mc     equal 100
+variable        swap_fraction equal 0.2
+variable        temperature_mc equal ${temperature}
+variable        temperature_mc equal 700
+variable        deltamu equal -0.70
+variable        target_concentration equal 0.02
+variable        kappa equal 1e3
+
+# general settings
+units           metal
+atom_style      atomic
+
+# set up structure
+boundary        p p p
+lattice         bcc 2.88
+Lattice spacing in x,y,z = 2.88 2.88 2.88
+region          box block 0 ${size}  0 ${size}  0 ${size}
+region          box block 0 20  0 ${size}  0 ${size}
+region          box block 0 20  0 20  0 ${size}
+region          box block 0 20  0 20  0 20
+create_box      2 box
+Created orthogonal box = (0 0 0) to (57.6 57.6 57.6)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box
+Created 16000 atoms
+  using lattice units in orthogonal box = (0 0 0) to (57.6 57.6 57.6)
+  create_atoms CPU = 0.001 seconds
+reset_timestep  0
+timestep        0.0025
+
+# set up interaction
+pair_style      eam/fs
+pair_coeff      * * FeCu.pasianot.eamfs Fe Cu
+
+# initialize velocities
+variable        double_temp equal ${temperature}*2
+variable        double_temp equal 700*2
+velocity        all create ${double_temp} 428459 dist gaussian
+velocity        all create 1400 428459 dist gaussian
+
+# what and how to run
+fix             integrate all npt                 temp ${temperature} ${temperature} 1.7                 aniso 0.0 0.0 1.5
+fix             integrate all npt                 temp 700 ${temperature} 1.7                 aniso 0.0 0.0 1.5
+fix             integrate all npt                 temp 700 700 1.7                 aniso 0.0 0.0 1.5
+fix             mc all sgcmc ${nsteps_mc} ${swap_fraction} ${temperature_mc} ${deltamu}                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 ${swap_fraction} ${temperature_mc} ${deltamu}                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 0.2 ${temperature_mc} ${deltamu}                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 0.2 700 ${deltamu}                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 0.2 700 -0.7                 randseed 324234                 variance ${kappa} ${target_concentration}
+fix             mc all sgcmc 100 0.2 700 -0.7                 randseed 324234                 variance 1000 ${target_concentration}
+fix             mc all sgcmc 100 0.2 700 -0.7                 randseed 324234                 variance 1000 0.02
+  SGC - Number of MD timesteps: 100
+  SGC - Fraction of swap atoms: 0.2
+  SGC - Temperature: %f
+  SGC - Chemical potential of species 2: -0.7
+  SGC - Random number seed: 324234
+  SGC - Kappa: 1000
+  SGC - Target concentration of species 2: 0.02
+  SGC - Target concentration of species 1: 0.98
+
+# set up output
+thermo          100
+thermo_style    custom step temp atoms pe press                 lx ly lz f_mc[1] f_mc[2] f_mc[3] f_mc[4]
+#dump            1 all custom 200 mc.*.dump id type x y z
+
+run             2000
+  SGC - Interaction radius: 5.50679
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.50679
+  ghost atom cutoff = 7.50679
+  binsize = 3.753395, bins = 16 16 16
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/fs, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) fix sgcmc, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.809 | 7.809 | 7.809 Mbytes
+   Step          Temp         Atoms        PotEng         Press            Lx             Ly             Lz          f_mc[1]        f_mc[2]        f_mc[3]        f_mc[4]    
+         0   1400               16000  -65889.786     -28854.541      57.6           57.6           57.6           0              0              1              0            
+       100   741.39222          16000  -64528.923      5317.2919      57.324639      57.32318       57.314928      19             3181           0.9988125      0.0011875    
+       200   691.21024          16000  -64405.429     -1238.5107      57.421346      57.415516      57.412006      16             3184           0.9978125      0.0021875    
+       300   686.85178          16000  -64377.312     -1816.799       57.424469      57.424335      57.425065      25             3175           0.996375       0.003625     
+       400   690.93203          16000  -64358.609      2211.7763      57.376246      57.38185       57.381742      16             3184           0.995375       0.004625     
+       500   696.77972          16000  -64350.3       -1583.8383      57.432929      57.426928      57.425935      22             3178           0.994125       0.005875     
+       600   694.13567          16000  -64320.831      144.2514       57.420097      57.403531      57.401394      19             3181           0.9930625      0.0069375    
+       700   691.79625          16000  -64295.155      384.47869      57.410637      57.412957      57.40707       25             3175           0.991625       0.008375     
+       800   692.12887          16000  -64270.053     -764.91901      57.415576      57.43037       57.428708      21             3179           0.9903125      0.0096875    
+       900   693.26555          16000  -64249.904      666.65335      57.408245      57.407059      57.417437      34             3166           0.9885625      0.0114375    
+      1000   697.97016          16000  -64230.234     -562.91022      57.432317      57.424316      57.423668      28             3172           0.9868125      0.0131875    
+      1100   686.52149          16000  -64177.536     -267.21801      57.429         57.434594      57.419878      35             3165           0.984875       0.015125     
+      1200   691.55047          16000  -64156.268      810.17844      57.422282      57.413529      57.422883      37             3163           0.9828125      0.0171875    
+      1300   691.91944          16000  -64124.602     -1012.7184      57.441793      57.433848      57.446947      32             3168           0.9810625      0.0189375    
+      1400   701.78807          16000  -64116.475      180.93518      57.425156      57.438679      57.419575      76             3124           0.9799375      0.0200625    
+      1500   692.75501          16000  -64080.481      176.96902      57.429275      57.442405      57.426519      81             3119           0.980125       0.019875     
+      1600   694.11818          16000  -64083.435     -785.49617      57.442143      57.432114      57.458304      86             3114           0.98           0.02         
+      1700   697.72576          16000  -64088.874      1227.5194      57.423225      57.408678      57.427056      75             3125           0.9800625      0.0199375    
+      1800   697.24171          16000  -64086.742     -1166.4832      57.447168      57.47416       57.425229      67             3133           0.98025        0.01975      
+      1900   699.53558          16000  -64092.97       214.99908      57.425459      57.437864      57.431139      86             3114           0.98025        0.01975      
+      2000   699.00277          16000  -64089.117      978.69672      57.429266      57.39107       57.448289      81             3119           0.9798125      0.0201875    
+Loop time of 15.2907 on 4 procs for 2000 steps with 16000 atoms
+
+Performance: 28.252 ns/day, 0.849 hours/ns, 130.798 timesteps/s, 2.093 Matom-step/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 14.31      | 14.404     | 14.479     |   1.6 | 94.20
+Neigh   | 0.090756   | 0.091006   | 0.091258   |   0.1 |  0.60
+Comm    | 0.27623    | 0.35113    | 0.44457    |  10.4 |  2.30
+Output  | 0.0006002  | 0.0013338  | 0.0035331  |   3.5 |  0.01
+Modify  | 0.38023    | 0.38128    | 0.38228    |   0.2 |  2.49
+Other   |            | 0.06148    |            |       |  0.40
+
+Nlocal:           4000 ave        4017 max        3970 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+Nghost:        8274.75 ave        8305 max        8257 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Neighs:         311257 ave      313506 max      308273 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+FullNghs:       622514 ave      626251 max      616896 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 2490056
+Ave neighs/atom = 155.6285
+Neighbor list builds = 6
+Dangerous builds = 0
+Total wall time: 0:00:15

src/.gitignore

@@ -920,6 +920,8 @@
 /fix_rigid_nvt_small.h
 /fix_rigid_small.cpp
 /fix_rigid_small.h
+/fix_sgcmc.cpp
+/fix_sgcmc.h
 /fix_shake.cpp
 /fix_shake.h
 /fix_shardlow.cpp

src/AMOEBA/amoeba_charge_transfer.cpp

@@ -15,7 +15,6 @@
 #include "pair_amoeba.h"
 
 #include "atom.h"
-#include "memory.h"
 #include "neigh_list.h"
 
 #include <cmath>

src/AMOEBA/amoeba_convolution.cpp

@@ -22,7 +22,9 @@
 #include "memory.h"
 #include "neighbor.h"
 #include "remap_wrap.h"
-#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/AMOEBA/amoeba_dispersion.cpp

@@ -18,10 +18,8 @@
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "fft3d_wrap.h"
 #include "math_const.h"
 #include "math_special.h"
-#include "memory.h"
 #include "neigh_list.h"
 
 #include <cmath>

src/AMOEBA/amoeba_file.cpp

@@ -17,14 +17,11 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
 #include "memory.h"
-#include "utils.h"
 #include "tokenizer.h"
 
 #include <cmath>
 #include <cstring>
-#include <cctype>
 
 using namespace LAMMPS_NS;
 

src/AMOEBA/amoeba_induce.cpp

@@ -19,16 +19,13 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fft3d_wrap.h"
 #include "fix_store_peratom.h"
 #include "math_const.h"
 #include "math_special.h"
-#include "memory.h"
 #include "my_page.h"
 #include "neigh_list.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/AMOEBA/amoeba_multipole.cpp

@@ -18,14 +18,11 @@
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "fft3d_wrap.h"
 #include "math_const.h"
 #include "math_special.h"
-#include "memory.h"
 #include "neigh_list.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/AMOEBA/amoeba_polar.cpp

@@ -18,10 +18,8 @@
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"
-#include "fft3d_wrap.h"
 #include "math_const.h"
 #include "math_special.h"
-#include "memory.h"
 #include "neigh_list.h"
 
 #include <cmath>

src/AMOEBA/amoeba_repulsion.cpp

@@ -16,7 +16,6 @@
 
 #include "atom.h"
 #include "comm.h"
-#include "memory.h"
 #include "neigh_list.h"
 
 #include <cmath>

src/AMOEBA/amoeba_utils.cpp

@@ -15,7 +15,6 @@
 #include "pair_amoeba.h"
 
 #include "atom.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "fix_store_peratom.h"

src/AMOEBA/atom_vec_amoeba.h

@@ -24,7 +24,7 @@ AtomStyle(amoeba,AtomVecAmoeba);
 
 namespace LAMMPS_NS {
 
-class AtomVecAmoeba : public AtomVec {
+class AtomVecAmoeba : virtual public AtomVec {
  public:
   AtomVecAmoeba(class LAMMPS *);
   ~AtomVecAmoeba() override;

src/AMOEBA/fix_amoeba_bitorsion.h

@@ -119,7 +119,7 @@ class FixAmoebaBiTorsion : public Fix {
   void chkttor(int, int, int, double &, double &, double &);
   void bcuint1(double *, double *, double *, double *, double, double, double, double, double,
                double, double &, double &, double &);
-  void bcucof(double *, double *, double *, double *, double, double, double[][4]);
+  void bcucof(double *, double *, double *, double *, double, double, double[4][4]);
 };
 }    // namespace LAMMPS_NS
 #endif

src/AMOEBA/improper_amoeba.cpp

@@ -22,7 +22,6 @@
 #include "memory.h"
 #include "neighbor.h"
 #include "pair.h"
-#include "update.h"
 
 #include <cmath>
 

src/AMOEBA/pair_amoeba.cpp

@@ -19,7 +19,6 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "fft3d_wrap.h"
 #include "fix.h"
 #include "fix_store_peratom.h"
 #include "force.h"
@@ -29,14 +28,11 @@
 #include "modify.h"
 #include "my_page.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "neighbor.h"
 #include "update.h"
-#include "utils.h"
 
-#include <cstdlib>
+#include <cmath>
 #include <cstring>
-#include <cctype>
 
 using namespace LAMMPS_NS;
 

src/ASPHERE/pair_ylz.cpp

@@ -256,7 +256,7 @@ void PairYLZ::coeff(int narg, char **arg)
 
 void PairYLZ::init_style()
 {
-  avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
+  avec = dynamic_cast<AtomVecEllipsoid *>(atom->style_match("ellipsoid"));
   if (!avec) error->all(FLERR, "Pair style ylz requires atom style ellipsoid");
 
   neighbor->request(this, instance_me);

src/AWPMD/atom_vec_wavepacket.h

@@ -24,7 +24,7 @@ AtomStyle(wavepacket,AtomVecWavepacket);
 
 namespace LAMMPS_NS {
 
-class AtomVecWavepacket : public AtomVec {
+class AtomVecWavepacket : virtual public AtomVec {
  public:
   AtomVecWavepacket(class LAMMPS *);
 

src/BPM/atom_vec_bpm_sphere.cpp

@@ -20,7 +20,6 @@
 #include "fix_adapt.h"
 #include "math_const.h"
 #include "modify.h"
-#include "utils.h"
 
 #include <cstring>
 

src/BPM/atom_vec_bpm_sphere.h

@@ -24,7 +24,7 @@ AtomStyle(bpm/sphere,AtomVecBPMSphere);
 
 namespace LAMMPS_NS {
 
-class AtomVecBPMSphere : public AtomVec {
+class AtomVecBPMSphere : virtual public AtomVec {
  public:
   AtomVecBPMSphere(class LAMMPS *);
   void process_args(int, char **) override;

src/BPM/bond_bpm.cpp

@@ -25,7 +25,8 @@
 #include "modify.h"
 #include "update.h"
 
-#include <vector>
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/BPM/bond_bpm.h

@@ -16,8 +16,6 @@
 
 #include "bond.h"
 
-#include <vector>
-
 namespace LAMMPS_NS {
 
 class BondBPM : public Bond {

src/BPM/bond_bpm_rotational.cpp

@@ -19,13 +19,13 @@
 #include "error.h"
 #include "fix_bond_history.h"
 #include "force.h"
-#include "math_const.h"
 #include "math_extra.h"
 #include "memory.h"
 #include "modify.h"
 #include "neighbor.h"
 
 #include <cmath>
+#include <cstring>
 
 #define EPSILON 1e-10
 

src/BPM/bond_bpm_spring.cpp

@@ -23,6 +23,9 @@
 #include "modify.h"
 #include "neighbor.h"
 
+#include <cmath>
+#include <cstring>
+
 #define EPSILON 1e-10
 
 using namespace LAMMPS_NS;

src/BPM/compute_nbond_atom.cpp

@@ -15,12 +15,8 @@
 
 #include "atom.h"
 #include "comm.h"
-#include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "update.h"
-
-#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -29,7 +25,7 @@ using namespace LAMMPS_NS;
 ComputeNBondAtom::ComputeNBondAtom(LAMMPS *_lmp, int narg, char **arg) :
     Compute(_lmp, narg, arg), nbond(nullptr)
 {
-  if (narg < 3) error->all(FLERR, "Illegal compute nbond/atom command");
+  if (narg < 3) utils::missing_cmd_args(FLERR, "compute nbond/atom", error);
 
   peratom_flag = 1;
   size_peratom_cols = 0;

src/BPM/fix_nve_bpm_sphere.cpp

@@ -14,13 +14,10 @@
 #include "fix_nve_bpm_sphere.h"
 
 #include "atom.h"
-#include "atom_vec.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
 #include "math_extra.h"
 
-#include <cmath>
 #include <cstring>
 
 using namespace LAMMPS_NS;

src/BPM/pair_bpm_spring.cpp

@@ -19,7 +19,8 @@
 #include "force.h"
 #include "memory.h"
 #include "neigh_list.h"
-#include "neighbor.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 

src/BROWNIAN/fix_brownian_asphere.cpp

@@ -27,6 +27,8 @@
 #include "math_extra.h"
 #include "random_mars.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/CG-DNA/atom_vec_oxdna.h

@@ -24,7 +24,7 @@ AtomStyle(oxdna,AtomVecOxdna);
 
 namespace LAMMPS_NS {
 
-class AtomVecOxdna : public AtomVec {
+class AtomVecOxdna : virtual public AtomVec {
  public:
   AtomVecOxdna(class LAMMPS *);
 

src/COLLOID/pair_brownian.cpp

@@ -92,7 +92,6 @@ void PairBrownian::compute(int eflag, int vflag)
   double prethermostat;
   double xl[3], a_sq, a_sh, a_pu, Fbmag;
   double p1[3], p2[3], p3[3];
-  int overlaps = 0;
 
   // This section of code adjusts R0/RT0/RS0 if necessary due to changes
   // in the volume fraction as a result of fix deform or moving walls
@@ -187,10 +186,6 @@ void PairBrownian::compute(int eflag, int vflag)
 
         h_sep = r - 2.0 * radi;
 
-        // check for overlaps
-
-        if (h_sep < 0.0) overlaps++;
-
         // if less than minimum gap, use minimum gap instead
 
         if (r < cut_inner[itype][jtype]) h_sep = cut_inner[itype][jtype] - 2.0 * radi;
@@ -336,9 +331,6 @@ void PairBrownian::compute(int eflag, int vflag)
     }
   }
 
-  int print_overlaps = 0;
-  if (print_overlaps && overlaps) printf("Number of overlaps=%d\n", overlaps);
-
   if (vflag_fdotr) virial_fdotr_compute();
 }
 

src/COLLOID/pair_brownian_poly.cpp

@@ -72,7 +72,6 @@ void PairBrownianPoly::compute(int eflag, int vflag)
   int nlocal = atom->nlocal;
 
   double vxmu2f = force->vxmu2f;
-  int overlaps = 0;
   double randr;
   double prethermostat;
   double xl[3],a_sq,a_sh,a_pu,Fbmag;
@@ -176,10 +175,6 @@ void PairBrownianPoly::compute(int eflag, int vflag)
 
         h_sep = r - radi-radj;
 
-        // check for overlaps
-
-        if (h_sep < 0.0) overlaps++;
-
         // if less than minimum gap, use minimum gap instead
 
         if (r < cut_inner[itype][jtype])

src/CORESHELL/compute_temp_cs.cpp

@@ -31,9 +31,6 @@
 #include "modify.h"
 #include "update.h"
 
-#include <cstring>
-
-
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */

src/DIELECTRIC/atom_vec_dielectric.h

@@ -24,7 +24,7 @@ AtomStyle(dielectric,AtomVecDielectric);
 
 namespace LAMMPS_NS {
 
-class AtomVecDielectric : public AtomVec {
+class AtomVecDielectric : virtual public AtomVec {
   friend class PairLJCutCoulDebyeDielectric;
   friend class PairLJLongCoulLongDielectric;
 

src/DIELECTRIC/msm_dielectric.cpp

@@ -20,7 +20,6 @@
 
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "grid3d.h"

src/DIELECTRIC/pppm_dielectric.cpp

@@ -20,10 +20,8 @@
 
 #include "atom.h"
 #include "atom_vec_dielectric.h"
-#include "comm.h"
 #include "domain.h"
 #include "error.h"
-#include "force.h"
 #include "grid3d.h"
 #include "math_const.h"
 #include "math_special.h"

src/DIELECTRIC/pppm_disp_dielectric.cpp

@@ -18,7 +18,6 @@
 
 #include "pppm_disp_dielectric.h"
 
-#include "angle.h"
 #include "atom.h"
 #include "atom_vec_dielectric.h"
 #include "domain.h"

src/DIFFRACTION/fix_saed_vtk.cpp

@@ -407,7 +407,6 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
 
     // Finding the intersection of the reciprical space and Ewald sphere
     int NROW1 = 0;
-    int NROW2 = 0;
     double dinv2 = 0.0;
     double r = 0.0;
     double K[3];
@@ -425,11 +424,9 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
               fprintf(fp,"%g\n",vector_total[NROW1]/norm);
               fflush(fp);
               NROW1++;
-              NROW2++;
             } else {
               fprintf(fp,"%d\n",-1);
               fflush(fp);
-              NROW2++;
             }
           }
         }
@@ -449,17 +446,14 @@ void FixSAEDVTK::invoke_vector(bigint ntimestep)
               if  ( (r >  (R_Ewald - dR_Ewald) ) && (r < (R_Ewald + dR_Ewald) )) {
                 fprintf(fp,"%g\n",vector_total[NROW1]/norm);
                 fflush(fp);
-                NROW2++;
                 NROW1++;
               } else {
                 fprintf(fp,"%d\n",-1);
                 fflush(fp);
-                NROW2++;
               }
             } else {
               fprintf(fp,"%d\n",-1);
               fflush(fp);
-              NROW2++;
             }
           }
         }

src/DIPOLE/atom_vec_dipole.h

@@ -24,7 +24,7 @@ AtomStyle(dipole,AtomVecDipole);
 
 namespace LAMMPS_NS {
 
-class AtomVecDipole : public AtomVec {
+class AtomVecDipole : virtual public AtomVec {
  public:
   AtomVecDipole(class LAMMPS *);
 

src/DPD-MESO/atom_vec_edpd.h

@@ -24,7 +24,7 @@ AtomStyle(edpd,AtomVecEDPD);
 
 namespace LAMMPS_NS {
 
-class AtomVecEDPD : public AtomVec {
+class AtomVecEDPD : virtual public AtomVec {
  public:
   AtomVecEDPD(class LAMMPS *);
   void init() override;

src/DPD-MESO/atom_vec_mdpd.h

@@ -24,7 +24,7 @@ AtomStyle(mdpd,AtomVecMDPD);
 
 namespace LAMMPS_NS {
 
-class AtomVecMDPD : public AtomVec {
+class AtomVecMDPD : virtual public AtomVec {
  public:
   AtomVecMDPD(class LAMMPS *);
   void init() override;

src/DPD-MESO/atom_vec_tdpd.h

@@ -24,7 +24,7 @@ AtomStyle(tdpd,AtomVecTDPD);
 
 namespace LAMMPS_NS {
 
-class AtomVecTDPD : public AtomVec {
+class AtomVecTDPD : virtual public AtomVec {
  public:
   AtomVecTDPD(class LAMMPS *);
   void process_args(int, char **) override;

src/DPD-REACT/atom_vec_dpd.h

@@ -24,7 +24,7 @@ AtomStyle(dpd,AtomVecDPD);
 
 namespace LAMMPS_NS {
 
-class AtomVecDPD : public AtomVec {
+class AtomVecDPD : virtual public AtomVec {
  public:
   AtomVecDPD(class LAMMPS *);
 
@@ -32,7 +32,7 @@ class AtomVecDPD : public AtomVec {
   void unpack_restart_init(int) override;
   void data_atom_post(int) override;
 
- private:
+ protected:
   double *rho, *dpdTheta;
   double *uCond, *uMech, *uChem;
   double *uCG, *uCGnew;

src/DPD-REACT/fix_rx.cpp

@@ -390,7 +390,6 @@ void FixRX::initSparse()
   int mxprod = 0;
   int mxreac = 0;
   int mxspec = 0;
-  int nIntegral = 0;
   for (int i = 0; i < nreactions; ++i) {
     int nreac_i = 0, nprod_i = 0;
     std::string pstr, rstr;
@@ -430,7 +429,6 @@ void FixRX::initSparse()
     mxreac = std::max( mxreac, nreac_i );
     mxprod = std::max( mxprod, nprod_i );
     mxspec = std::max( mxspec, nreac_i + nprod_i );
-    if (allAreIntegral) nIntegral++;
   }
 
   if (comm->me == 0 && Verbosity > 1) {

src/EFF/atom_vec_electron.cpp

@@ -20,6 +20,8 @@
 #include "atom.h"
 #include "citeme.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 static const char cite_user_eff_package[] =

src/EFF/atom_vec_electron.h

@@ -24,7 +24,7 @@ AtomStyle(electron,AtomVecElectron);
 
 namespace LAMMPS_NS {
 
-class AtomVecElectron : public AtomVec {
+class AtomVecElectron : virtual public AtomVec {
  public:
   AtomVecElectron(class LAMMPS *);
 

src/EFF/compute_temp_region_eff.cpp

@@ -141,12 +141,6 @@ double ComputeTempRegionEff::compute_scalar()
   if (dof < 0.0 && tarray_all[0] > 0.0)
     error->all(FLERR, "Temperature compute degrees of freedom < 0");
 
-  int one = 0;
-  for (int i = 0; i < nlocal; i++)
-    if (mask[i] & groupbit && region->match(x[i][0], x[i][1], x[i][2])) {
-      if (abs(spin[i]) == 1) one++;
-    }
-
   if (dof > 0.0)
     scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz);
   else

src/ELECTRODE/electrode_matrix.cpp

@@ -29,6 +29,9 @@
 #include "neigh_list.h"
 #include "pair.h"
 
+#include <cmath>
+#include <cstring>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/ELECTRODE/electrode_vector.cpp

@@ -29,6 +29,9 @@
 #include "neigh_list.h"
 #include "pair.h"
 
+#include <cmath>
+#include <exception>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/ELECTRODE/ewald_electrode.cpp

@@ -18,6 +18,7 @@
 #include "ewald_electrode.h"
 
 #include "atom.h"
+#include "boundary_correction.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
@@ -32,7 +33,6 @@
 
 #include <algorithm>
 #include <cmath>
-#include <limits>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/ELECTRODE/fix_electrode_conp.cpp

@@ -20,7 +20,6 @@
 #include "atom.h"
 #include "citeme.h"
 #include "comm.h"
-#include "compute.h"
 #include "domain.h"
 #include "electrode_accel_interface.h"
 #include "electrode_math.h"
@@ -37,12 +36,15 @@
 #include "neigh_request.h"
 #include "neighbor.h"
 #include "pair.h"
-#include "pointers.h"
 #include "text_file_reader.h"
 #include "variable.h"
 
+#include <algorithm>
 #include <cassert>
-#include <numeric>
+#include <cmath>
+#include <cstring>
+#include <exception>
+#include <utility>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -867,7 +869,7 @@ void FixElectrodeConp::update_charges()
   accel_interface->intel_pack_buffers();
 }
 
-std::vector<double> FixElectrodeConp::ele_ele_interaction(std::vector<double> q_local)
+std::vector<double> FixElectrodeConp::ele_ele_interaction(const std::vector<double>& q_local)
 {
   assert(q_local.size() == nlocalele);
   assert(algo == Algo::CG || algo == Algo::MATRIX_CG);
@@ -1415,14 +1417,13 @@ void FixElectrodeConp::gather_list_iele()
   }
   taglist_local.clear();
   iele_to_group_local.clear();
-  for (int i = 0, iele = 0; i < nlocal; i++) {
+  for (int i = 0; i < nlocal; i++) {
     if (mask[i] & groupbit) {
       tagint const t = tag[i];
       if (matrix_algo) list_iele.push_back(tag_to_iele[t]);
       taglist_local.push_back(t);
       for (int g = 0; g < num_of_groups; g++)
         if (mask[i] & group_bits[g]) iele_to_group_local.push_back(g);
-      iele++;
     }
   }
   nlocalele = static_cast<int>(taglist_local.size());    // just for safety

src/ELECTRODE/fix_electrode_conp.h

@@ -26,15 +26,19 @@ FixStyle(electrode/conp, FixElectrodeConp);
 #ifndef LMP_FIX_ELECTRODE_CONP_H
 #define LMP_FIX_ELECTRODE_CONP_H
 
-#include "electrode_accel_interface.h"
 #include "fix.h"
 
-#include <algorithm>
 #include <map>
 #include <memory>
 #include <unordered_map>
 
 namespace LAMMPS_NS {
+// forward decls
+
+class ElectrodeAccelInterface;
+class ElectrodeVector;
+class NeighList;
+class Pair;
 
 class FixElectrodeConp : public Fix {
 
@@ -75,7 +79,7 @@ class FixElectrodeConp : public Fix {
   virtual std::vector<double> constraint_projection(std::vector<double>);
   virtual std::vector<double> constraint_correction(std::vector<double>);
   virtual void compute_macro_matrices();
-  std::vector<double> ele_ele_interaction(std::vector<double>);
+  std::vector<double> ele_ele_interaction(const std::vector<double> &);
   std::vector<double> group_psi;
   std::vector<int> group_bits;
   std::vector<int> groups;
@@ -102,7 +106,7 @@ class FixElectrodeConp : public Fix {
  private:
   std::string output_file_inv, output_file_mat, output_file_vec;
   std::string input_file_inv, input_file_mat;
-  class ElectrodeVector *elyt_vector, *elec_vector;
+  ElectrodeVector *elyt_vector, *elec_vector;
   double **capacitance, **elastance;
   bool read_inv, read_mat, write_inv, write_mat, write_vec;
   bool matrix_algo, need_array_compute, need_elec_vector;
@@ -121,8 +125,8 @@ class FixElectrodeConp : public Fix {
   void compute_sd_vectors();
   void compute_sd_vectors_ffield();
   int groupnum_from_name(char *);
-  class Pair *pair;
+  Pair *pair;
-  class NeighList *mat_neighlist, *vec_neighlist;
+  NeighList *mat_neighlist, *vec_neighlist;
   std::vector<int> etypes;
   int mat_request, vec_request;
   void request_etypes_neighlists();

src/ELECTRODE/fix_electrode_thermo.cpp

@@ -20,12 +20,13 @@
 #include "atom.h"
 #include "error.h"
 #include "fix_electrode_conp.h"
-#include "force.h"
 #include "input.h"
 #include "random_mars.h"
 #include "update.h"
 #include "variable.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 
 #define NUM_GROUPS 2

src/ELECTRODE/slab_2d.cpp

@@ -18,12 +18,12 @@
 #include "slab_2d.h"
 
 #include "atom.h"
-#include "comm.h"
 #include "domain.h"
 #include "force.h"
 #include "kspace.h"
 #include "math_const.h"
-#include "memory.h"
+
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/ELECTRODE/slab_dipole.cpp

@@ -18,12 +18,13 @@
 #include "slab_dipole.h"
 
 #include "atom.h"
-#include "comm.h"
 #include "domain.h"
 #include "force.h"
 #include "kspace.h"
 #include "math_const.h"
 
+#include <cmath>
+
 using namespace LAMMPS_NS;
 using namespace MathConst;
 

src/ELECTRODE/wire_dipole.cpp

@@ -19,7 +19,6 @@
 
 #include "atom.h"
 #include "comm.h"
-#include "domain.h"
 #include "force.h"
 #include "math_const.h"
 

src/EXTRA-COMPUTE/compute_basal_atom.cpp

@@ -31,7 +31,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/EXTRA-COMPUTE/compute_born_matrix.cpp

@@ -33,10 +33,8 @@
 #include "modify.h"
 #include "molecule.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "neighbor.h"
 #include "pair.h"
-#include "universe.h"
 #include "update.h"
 
 #include <cmath>

src/EXTRA-COMPUTE/compute_stress_cartesian.cpp

@@ -20,7 +20,6 @@
 #include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "modify.h"
 #include "neigh_list.h"
 #include "neighbor.h"
 #include "pair.h"

src/EXTRA-COMPUTE/compute_stress_cylinder.cpp

@@ -21,7 +21,6 @@
 #include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
-#include "modify.h"
 #include "neigh_list.h"
 #include "neighbor.h"
 #include "pair.h"
@@ -29,7 +28,6 @@
 
 #include <cmath>
 #include <cstring>
-#include <mpi.h>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/EXTRA-COMPUTE/compute_stress_spherical.cpp

@@ -19,19 +19,15 @@
 #include "domain.h"
 #include "error.h"
 #include "force.h"
-#include "lattice.h"
 #include "math_const.h"
 #include "math_special.h"
 #include "memory.h"
-#include "modify.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "neighbor.h"
 #include "pair.h"
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/EXTRA-DUMP/dump_yaml.cpp

@@ -20,6 +20,8 @@
 #include "thermo.h"
 #include "update.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */

src/EXTRA-FIX/fix_ave_correlate_long.cpp

@@ -36,7 +36,6 @@
 #include "update.h"
 #include "variable.h"
 
-#include <cmath>
 #include <cstring>
 
 using namespace LAMMPS_NS;

src/EXTRA-FIX/fix_viscous_sphere.cpp

@@ -14,11 +14,9 @@
 #include "fix_viscous_sphere.h"
 
 #include "atom.h"
-#include "comm.h"
 #include "error.h"
 #include "input.h"
 #include "memory.h"
-#include "modify.h"
 #include "respa.h"
 #include "update.h"
 #include "variable.h"

src/EXTRA-MOLECULE/dihedral_nharmonic.cpp

@@ -25,7 +25,6 @@
 #include "force.h"
 #include "memory.h"
 #include "neighbor.h"
-#include "domain.h"
 
 #include <cmath>
 

src/FEP/compute_fep_ta.cpp

@@ -30,7 +30,6 @@
 #include "kspace.h"
 #include "memory.h"
 #include "modify.h"
-#include "neighbor.h"
 #include "pair.h"
 #include "timer.h"
 #include "update.h"

src/GPU/fix_gpu.cpp

@@ -120,8 +120,8 @@ FixGPU::FixGPU(LAMMPS *lmp, int narg, char **arg) :
 
   // If ngpu is 0, autoset ngpu to the number of devices per node matching
   // best device
-  int ngpu = atoi(arg[3]);
+  int ngpu = utils::inumeric(FLERR, arg[3], false, lmp);
-  if (ngpu < 0) error->all(FLERR,"Illegal package gpu command");
+  if (ngpu < 0) error->all(FLERR,"Illegal number of GPUs ({}) in package gpu command", ngpu);
 
   // Negative value indicate GPU package should find the best device ID
   int first_gpu_id = -1;

src/GRANULAR/compute_contact_atom.cpp

@@ -25,8 +25,6 @@
 #include "neighbor.h"
 #include "update.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */

src/GRANULAR/pair_gran_hooke_history.cpp

@@ -27,7 +27,6 @@
 #include "memory.h"
 #include "modify.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "neighbor.h"
 #include "update.h"
 

src/GRANULAR/pair_granular.cpp

@@ -32,7 +32,6 @@
 #include "memory.h"
 #include "modify.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "neighbor.h"
 #include "update.h"
 

src/INTERLAYER/pair_drip.cpp

@@ -28,7 +28,6 @@
 #include "force.h"
 #include "memory.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
 #include "neighbor.h"
 #include "potential_file_reader.h"
 

src/INTERLAYER/pair_ilp_tmd.cpp

@@ -22,15 +22,12 @@
 
 #include "atom.h"
 #include "citeme.h"
-#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "interlayer_taper.h"
 #include "memory.h"
 #include "my_page.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "neighbor.h"
 
 #include <cmath>
 #include <cstring>

src/INTERLAYER/pair_saip_metal.cpp

@@ -26,8 +26,6 @@
 #include "force.h"
 #include "interlayer_taper.h"
 #include "neigh_list.h"
-#include "neigh_request.h"
-#include "neighbor.h"
 
 #include <cmath>
 #include <cstring>

src/KIM/kim_param.cpp

@@ -155,11 +155,9 @@ void KimParam::command(int narg, char **arg)
 
   std::string kim_param_get_set(arg[0]);
 
-  if ((kim_param_get_set != "get") && (kim_param_get_set != "set")) {
+  if ((kim_param_get_set != "get") && (kim_param_get_set != "set"))
-    std::string msg("Incorrect arguments in 'kim param' command.\n");
+    error->all(FLERR, "Incorrect arguments in 'kim param' command.\n"
-    msg += "'kim param get/set' is mandatory";
+               "'kim param get/set' is mandatory");
-    error->all(FLERR, msg);
-  }
 
   int const ifix = modify->find_fix("KIM_MODEL_STORE");
   if (ifix >= 0) {
@@ -170,8 +168,7 @@ void KimParam::command(int narg, char **arg)
             fix_store->getptr("simulator_model"));
 
     if (simulatorModel)
-      error->all(FLERR,
+      error->all(FLERR, "'kim param' can only be used with a KIM Portable Model");
-        "'kim param' can only be used with a KIM Portable Model");
   }
 
   input->write_echo(fmt::format("#=== BEGIN kim param {} ==================="
@@ -196,13 +193,10 @@ void KimParam::command(int narg, char **arg)
     } else
       error->all(FLERR, "Pair style is defined, but there is "
                         "no match for kim style in lammps");
-  } else {
+  } else
-    auto msg = fmt::format("Illegal 'kim param {0}' command.\nTo {0} the new "
+    error->all(FLERR, "Illegal 'kim param {0}' command.\nTo {0} the new parameter values, "
-                           "parameter values, pair style must be assigned.\n"
+               "pair style must be assigned.\nMust use 'kim interactions' or 'pair_style kim' "
-                           "Must use 'kim interactions' or 'pair_style kim' "
                "before 'kim param {0}'", kim_param_get_set);
-    error->all(FLERR, msg);
-  }
 
   // Get the number of mutable parameters in the kim model
   int numberOfParameters(0);
@@ -243,12 +237,9 @@ void KimParam::command(int narg, char **arg)
           if (paramname == str_name_str) break;
         }
 
-        if (param_index >= numberOfParameters) {
+        if (param_index >= numberOfParameters)
-          auto msg = fmt::format("Wrong argument in 'kim param get' command.\n"
+          error->all(FLERR, "Wrong argument in 'kim param get' command.\n"
-                                 "This Model does not have the requested '{}' "
+                     "This Model does not have the requested '{}' parameter", paramname);
-                                 "parameter", paramname);
-          error->all(FLERR, msg);
-        }
 
         // Get the index_range for the requested parameter
         int nlbound(0);
@@ -259,12 +250,9 @@ void KimParam::command(int narg, char **arg)
 
           // Check to see if the indices range contains
           // only integer numbers and/or range :
-          if (argtostr.find_first_not_of("0123456789:") != std::string::npos) {
+          if (argtostr.find_first_not_of("0123456789:") != std::string::npos)
-            auto msg = fmt::format("Illegal index_range.\nExpected integer "
+            error->all(FLERR, "Illegal index_range.\nExpected integer parameter(s) instead "
-                                   "parameter(s) instead of '{}' in "
+                       "of '{}' in index_range", argtostr);
-                                   "index_range", argtostr);
-            error->all(FLERR, msg);
-          }
 
           std::string::size_type npos = argtostr.find(':');
           if (npos != std::string::npos) {
@@ -273,30 +261,20 @@ void KimParam::command(int narg, char **arg)
             nlbound = atoi(words[0].c_str());
             nubound = atoi(words[1].c_str());
 
-            if (nubound < 1 || nubound > extent ||
+            if ((nubound < 1) || (nubound > extent) || (nlbound < 1) || (nlbound > nubound))
-                nlbound < 1 || nlbound > nubound) {
+              error->all(FLERR, "Illegal index_range '{}-{}' for '{}' parameter with the "
-              auto msg = fmt::format("Illegal index_range '{}-{}' for '{}' "
+                         "extent of '{}'",nlbound, nubound, paramname, extent);
-                                     "parameter with the extent of '{}'",
-                                     nlbound, nubound, paramname, extent);
-              error->all(FLERR, msg);
-            }
           } else {
             nlbound = atoi(argtostr.c_str());
 
-            if (nlbound < 1 || nlbound > extent) {
+            if (nlbound < 1 || nlbound > extent)
-              auto msg = fmt::format("Illegal index '{}' for '{}' parameter "
+              error->all(FLERR, "Illegal index '{}' for '{}' parameter with the extent of '{}'",
-                                     "with the extent of '{}'", nlbound,
+                         nlbound, paramname, extent);
-                                     paramname, extent);
-              error->all(FLERR, msg);
-            }
-
             nubound = nlbound;
           }
-        } else {
+        } else
-          std::string msg("Wrong number of arguments in 'kim param get' ");
+          error->all(FLERR, "Wrong number of arguments in 'kim param get' command.\n"
-          msg += "command.\nIndex range after parameter name is mandatory";
+                     "Index range after parameter name is mandatory");
-          error->all(FLERR, msg);
-        }
 
         int const nvars = nubound - nlbound + 1;
         std::vector<std::string> varsname;
@@ -304,15 +282,11 @@ void KimParam::command(int narg, char **arg)
         if (i < narg) {
           // Get the variable/variable_base name
           varname = std::string(arg[i++]);
-          if ((varname == "split") ||
+          if ((varname == "split") || (varname == "list") || (varname == "explicit"))
-              (varname == "list") ||
+            error->all(FLERR, "Illegal variable name '{}' in 'kim param get'", varname);
-              (varname == "explicit"))
+        } else
-            error->all(FLERR, "Illegal variable name in 'kim param get'");
+          error->all(FLERR, "Wrong number of arguments in 'kim param get' command.\n"
-        } else {
+                     "The LAMMPS variable name is mandatory");
-          std::string msg("Wrong number of arguments in 'kim param get' ");
-          msg += "command.\nThe LAMMPS variable name is mandatory";
-          error->all(FLERR, msg);
-        }
 
         // indicator flag for list request
         bool list_requested(false);
@@ -337,28 +311,22 @@ void KimParam::command(int narg, char **arg)
               --i;
               for (int j = 0; j < nvars; ++j, ++i) {
                 varsname[j] = std::string(arg[i]);
-                if (varsname[j] == "split" || varsname[j] == "list" ||
+                if (varsname[j] == "split" || varsname[j] == "list" || varsname[j] == "explicit")
-                    varsname[j] == "explicit")
+                  error->all(FLERR, "Illegal variable name '{}' in 'kim param get'", varsname[j]);
-                  error->all(FLERR, "Illegal variable name in 'kim param get'");
               }
               if (i < narg) {
                 formatarg = std::string(arg[i]);
                 if (formatarg == "explicit") ++i;
               }
             } else {
-              auto msg =
+              error->all(FLERR, "Wrong number of arguments in 'kim param get' command.\n"
-                fmt::format("Wrong number of arguments in 'kim param get' "
+                         "The LAMMPS '{}' variable names or '{} split' is mandatory",
-                            "command.\nThe LAMMPS '{}' variable names or "
+                         nvars, varname);
-                            "'{} split' is mandatory", nvars, varname);
-              error->all(FLERR, msg);
-            }
-          } else {
-            auto msg =
-              fmt::format("Wrong number of arguments in 'kim param get' "
-                          "command.\nThe LAMMPS '{}' variable names or "
-                          "'{} split/list' is mandatory", nvars, varname);
-            error->all(FLERR, msg);
             }
+          } else
+            error->all(FLERR, "Wrong number of arguments in 'kim param get' command.\n"
+                       "The LAMMPS '{}' variable names or '{} split/list' is mandatory",
+                       nvars, varname);
         } else {
           varsname.resize(1);
           if (i < narg) {

src/KIM/pair_kim.cpp

@@ -483,15 +483,13 @@ void PairKIM::coeff(int narg, char **arg)
           nlbound = atoi(words[0].c_str());
           nubound = atoi(words[1].c_str());
 
-          if (nubound < 1 || nubound > extent ||
+          if ((nubound < 1) || (nubound > extent) || (nlbound < 1) || (nlbound > nubound))
-              nlbound < 1 || nlbound > nubound)
+            error->all(FLERR,"Illegal index_range '{}-{}' for '{}' parameter with the extent of '{}'",
-            error->all(FLERR,"Illegal index_range '{}-{}' for '{}' "
-                       "parameter with the extent of '{}'",
                        nlbound, nubound, paramname, extent);
         } else {
           nlbound = atoi(argtostr.c_str());
 
-          if (nlbound < 1 || nlbound > extent)
+          if ((nlbound < 1) || (nlbound > extent))
             error->all(FLERR,"Illegal index '{}' for '{}' parameter with the extent of '{}'",
                        nlbound, paramname, extent);
 
@@ -1081,8 +1079,7 @@ void PairKIM::set_kim_model_has_flags()
     KIM_ComputeArguments_GetArgumentSupportStatus(
       pargs, computeArgumentName, &supportStatus);
 
-    if (KIM_ComputeArgumentName_Equal(computeArgumentName,
+    if (KIM_ComputeArgumentName_Equal(computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialEnergy))
-                                      KIM_COMPUTE_ARGUMENT_NAME_partialEnergy))
       kim_model_support_for_energy = supportStatus;
     else if (KIM_ComputeArgumentName_Equal(
                computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialForces))
@@ -1095,17 +1092,14 @@ void PairKIM::set_kim_model_has_flags()
                computeArgumentName,
                KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial))
       kim_model_support_for_particleVirial = supportStatus;
-    else if (KIM_SupportStatus_Equal(supportStatus,
+    else if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required)) {
-                                     KIM_SUPPORT_STATUS_required)) {
+      error->all(FLERR, "KIM Model requires unsupported compute argument: {}",
-      std::string msg("KIM Model requires unsupported compute argument: ");
+                 KIM_ComputeArgumentName_ToString(computeArgumentName));
-      msg += KIM_ComputeArgumentName_ToString(computeArgumentName);
-      error->all(FLERR,msg);
     }
   }
 
   if (comm->me == 0) {
-    if (KIM_SupportStatus_Equal(kim_model_support_for_energy,
+    if (KIM_SupportStatus_Equal(kim_model_support_for_energy, KIM_SUPPORT_STATUS_notSupported))
-                                KIM_SUPPORT_STATUS_notSupported))
       error->warning(FLERR,"KIM Model does not provide 'partialEnergy'; Potential energy will be zero");
 
     if (KIM_SupportStatus_Equal(kim_model_support_for_forces,

src/KOKKOS/Install.sh

@@ -64,8 +64,8 @@ action atom_vec_bond_kokkos.cpp atom_vec_bond.cpp
 action atom_vec_bond_kokkos.h atom_vec_bond.h
 action atom_vec_charge_kokkos.cpp
 action atom_vec_charge_kokkos.h
-action atom_vec_spin_kokkos.cpp
+action atom_vec_spin_kokkos.cpp atom_vec_spin.cpp
-action atom_vec_spin_kokkos.h
+action atom_vec_spin_kokkos.h atom_vec_spin.h
 action atom_vec_dpd_kokkos.cpp atom_vec_dpd.cpp
 action atom_vec_dpd_kokkos.h atom_vec_dpd.h
 action atom_vec_full_kokkos.cpp atom_vec_full.cpp

src/KOKKOS/atom_kokkos.cpp

@@ -104,23 +104,23 @@ AtomKokkos::~AtomKokkos()
 
 void AtomKokkos::sync(const ExecutionSpace space, unsigned int mask)
 {
-  if (space == Device && lmp->kokkos->auto_sync) ((AtomVecKokkos *) avec)->modified(Host, mask);
+  if (space == Device && lmp->kokkos->auto_sync) avecKK->modified(Host, mask);
 
-  ((AtomVecKokkos *) avec)->sync(space, mask);
+  avecKK->sync(space, mask);
 }
 
 /* ---------------------------------------------------------------------- */
 
 void AtomKokkos::modified(const ExecutionSpace space, unsigned int mask)
 {
-  ((AtomVecKokkos *) avec)->modified(space, mask);
+  avecKK->modified(space, mask);
 
-  if (space == Device && lmp->kokkos->auto_sync) ((AtomVecKokkos *) avec)->sync(Host, mask);
+  if (space == Device && lmp->kokkos->auto_sync) avecKK->sync(Host, mask);
 }
 
 void AtomKokkos::sync_overlapping_device(const ExecutionSpace space, unsigned int mask)
 {
-  ((AtomVecKokkos *) avec)->sync_overlapping_device(space, mask);
+  avecKK->sync_overlapping_device(space, mask);
 }
 /* ---------------------------------------------------------------------- */
 
@@ -380,5 +380,8 @@ AtomVec *AtomKokkos::new_avec(const std::string &style, int trysuffix, int &sfla
 {
   AtomVec *avec = Atom::new_avec(style, trysuffix, sflag);
   if (!avec->kokkosable) error->all(FLERR, "KOKKOS package requires a kokkos enabled atom_style");
+
+  avecKK = dynamic_cast<AtomVecKokkos*>(avec);
+
   return avec;
 }

src/KOKKOS/atom_kokkos.h

@@ -78,6 +78,8 @@ class AtomKokkos : public Atom {
   DAT::tdual_int_scalar k_error_flag;
   dual_hash_type k_map_hash;
 
+  class AtomVecKokkos* avecKK;
+
   // map lookup function inlined for efficiency
   // return -1 if no map defined
 

src/KOKKOS/atom_vec_angle_kokkos.cpp

@@ -27,27 +27,10 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-AtomVecAngleKokkos::AtomVecAngleKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
+AtomVecAngleKokkos::AtomVecAngleKokkos(LAMMPS *lmp) : AtomVec(lmp),
+AtomVecKokkos(lmp), AtomVecAngle(lmp)
 {
-  molecular = Atom::MOLECULAR;
-  bonds_allow = angles_allow = 1;
-  mass_type = PER_TYPE;
 
-  comm_x_only = comm_f_only = 1;
-  size_forward = 3;
-  size_reverse = 3;
-  size_border = 7;
-  size_velocity = 3;
-  size_data_atom = 6;
-  size_data_vel = 4;
-  xcol_data = 4;
-
-  atom->molecule_flag = 1;
-
-  k_count = DAT::tdual_int_1d("atom::k_count",1);
-  atomKK = (AtomKokkos *) atom;
-  commKK = (CommKokkos *) comm;
-  buffer = nullptr;
 }
 
 /* ----------------------------------------------------------------------
@@ -172,52 +155,6 @@ void AtomVecAngleKokkos::grow_pointers()
   h_angle_atom3 = atomKK->k_angle_atom3.h_view;
 }
 
-/* ----------------------------------------------------------------------
-   copy atom I info to atom J
-------------------------------------------------------------------------- */
-
-void AtomVecAngleKokkos::copy(int i, int j, int delflag)
-{
-  int k;
-
-  h_tag[j] = h_tag[i];
-  h_type[j] = h_type[i];
-  mask[j] = mask[i];
-  h_image[j] = h_image[i];
-  h_x(j,0) = h_x(i,0);
-  h_x(j,1) = h_x(i,1);
-  h_x(j,2) = h_x(i,2);
-  h_v(j,0) = h_v(i,0);
-  h_v(j,1) = h_v(i,1);
-  h_v(j,2) = h_v(i,2);
-
-  h_molecule(j) = h_molecule(i);
-
-  h_num_bond(j) = h_num_bond(i);
-  for (k = 0; k < h_num_bond(j); k++) {
-    h_bond_type(j,k) = h_bond_type(i,k);
-    h_bond_atom(j,k) = h_bond_atom(i,k);
-  }
-
-  h_nspecial(j,0) = h_nspecial(i,0);
-  h_nspecial(j,1) = h_nspecial(i,1);
-  h_nspecial(j,2) = h_nspecial(i,2);
-  for (k = 0; k < h_nspecial(j,2); k++)
-    h_special(j,k) = h_special(i,k);
-
-  h_num_angle(j) = h_num_angle(i);
-  for (k = 0; k < h_num_angle(j); k++) {
-    h_angle_type(j,k) = h_angle_type(i,k);
-    h_angle_atom1(j,k) = h_angle_atom1(i,k);
-    h_angle_atom2(j,k) = h_angle_atom2(i,k);
-    h_angle_atom3(j,k) = h_angle_atom3(i,k);
-  }
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
-}
-
 /* ---------------------------------------------------------------------- */
 
 template<class DeviceType,int PBC_FLAG,int TRICLINIC>
@@ -508,171 +445,6 @@ void AtomVecAngleKokkos::unpack_comm_kokkos(const int &n, const int &first,
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecAngleKokkos::pack_comm(int n, int *list, double *buf,
-                                 int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
-      dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
-      dz = pbc[2]*domain->zprd;
-    }
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0) + dx;
-      buf[m++] = h_x(j,1) + dy;
-      buf[m++] = h_x(j,2) + dz;
-    }
-  }
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::pack_comm_vel(int n, int *list, double *buf,
-                                     int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz,dvx,dvy,dvz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-      buf[m++] = h_v(j,0);
-      buf[m++] = h_v(j,1);
-      buf[m++] = h_v(j,2);
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
-      dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
-      dz = pbc[2]*domain->zprd;
-    }
-    if (!deform_vremap) {
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        buf[m++] = h_v(j,0);
-        buf[m++] = h_v(j,1);
-        buf[m++] = h_v(j,2);
-      }
-    } else {
-      dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
-      dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
-      dvz = pbc[2]*h_rate[2];
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        if (mask[i] & deform_groupbit) {
-          buf[m++] = h_v(j,0) + dvx;
-          buf[m++] = h_v(j,1) + dvy;
-          buf[m++] = h_v(j,2) + dvz;
-        } else {
-          buf[m++] = h_v(j,0);
-          buf[m++] = h_v(j,1);
-          buf[m++] = h_v(j,2);
-        }
-      }
-    }
-  }
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomVecAngleKokkos::unpack_comm(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomVecAngleKokkos::unpack_comm_vel(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-    h_v(i,0) = buf[m++];
-    h_v(i,1) = buf[m++];
-    h_v(i,2) = buf[m++];
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::pack_reverse(int n, int first, double *buf)
-{
-  if (n > 0)
-    atomKK->sync(Host,F_MASK);
-
-  int m = 0;
-  const int last = first + n;
-  for (int i = first; i < last; i++) {
-    buf[m++] = h_f(i,0);
-    buf[m++] = h_f(i,1);
-    buf[m++] = h_f(i,2);
-  }
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomVecAngleKokkos::unpack_reverse(int n, int *list, double *buf)
-{
-  if (n > 0)
-    atomKK->modified(Host,F_MASK);
-
-  int m = 0;
-  for (int i = 0; i < n; i++) {
-    const int j = list[i];
-    h_f(j,0) += buf[m++];
-    h_f(j,1) += buf[m++];
-    h_f(j,2) += buf[m++];
-  }
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType,int PBC_FLAG>
 struct AtomVecAngleKokkos_PackBorder {
   typedef DeviceType device_type;
@@ -774,149 +546,6 @@ int AtomVecAngleKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecAngleKokkos::pack_border(int n, int *list, double *buf,
-                                   int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = ubuf(h_molecule(j)).d;
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0];
-      dy = pbc[1];
-      dz = pbc[2];
-    }
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0) + dx;
-      buf[m++] = h_x(j,1) + dy;
-      buf[m++] = h_x(j,2) + dz;
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = ubuf(h_molecule(j)).d;
-    }
-  }
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
-
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::pack_border_vel(int n, int *list, double *buf,
-                                       int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz,dvx,dvy,dvz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = ubuf(h_molecule(j)).d;
-      buf[m++] = h_v(j,0);
-      buf[m++] = h_v(j,1);
-      buf[m++] = h_v(j,2);
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0];
-      dy = pbc[1];
-      dz = pbc[2];
-    }
-    if (!deform_vremap) {
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        buf[m++] = ubuf(h_tag(j)).d;
-        buf[m++] = ubuf(h_type(j)).d;
-        buf[m++] = ubuf(h_mask(j)).d;
-        buf[m++] = ubuf(h_molecule(j)).d;
-        buf[m++] = h_v(j,0);
-        buf[m++] = h_v(j,1);
-        buf[m++] = h_v(j,2);
-      }
-    } else {
-      dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
-      dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
-      dvz = pbc[2]*h_rate[2];
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        buf[m++] = ubuf(h_tag(j)).d;
-        buf[m++] = ubuf(h_type(j)).d;
-        buf[m++] = ubuf(h_mask(j)).d;
-        buf[m++] = ubuf(h_molecule(j)).d;
-        if (mask[i] & deform_groupbit) {
-          buf[m++] = h_v(j,0) + dvx;
-          buf[m++] = h_v(j,1) + dvy;
-          buf[m++] = h_v(j,2) + dvz;
-        } else {
-          buf[m++] = h_v(j,0);
-          buf[m++] = h_v(j,1);
-          buf[m++] = h_v(j,2);
-        }
-      }
-    }
-  }
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
-
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::pack_border_hybrid(int n, int *list, double *buf)
-{
-  int i,j,m;
-
-  m = 0;
-  for (i = 0; i < n; i++) {
-    j = list[i];
-    buf[m++] = h_molecule(j);
-  }
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecAngleKokkos_UnpackBorder {
   typedef DeviceType device_type;
@@ -977,78 +606,6 @@ void AtomVecAngleKokkos::unpack_border_kokkos(const int &n, const int &first,
 
 /* ---------------------------------------------------------------------- */
 
-void AtomVecAngleKokkos::unpack_border(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  while (last > nmax) grow(0);
-
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-    h_tag(i) =  (tagint)  ubuf(buf[m++]).i;
-    h_type(i) = (int) ubuf(buf[m++]).i;
-    h_mask(i) = (int) ubuf(buf[m++]).i;
-    h_molecule(i) = (tagint) ubuf(buf[m++]).i;
-  }
-
-  atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->
-        unpack_border(n,first,&buf[m]);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomVecAngleKokkos::unpack_border_vel(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  while (last > nmax) grow(0);
-
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-    h_tag(i) =  (tagint)  ubuf(buf[m++]).i;
-    h_type(i) = (int) ubuf(buf[m++]).i;
-    h_mask(i) = (int) ubuf(buf[m++]).i;
-    h_molecule(i) = (tagint) ubuf(buf[m++]).i;
-    h_v(i,0) = buf[m++];
-    h_v(i,1) = buf[m++];
-    h_v(i,2) = buf[m++];
-  }
-
-  atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|V_MASK);
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->
-        unpack_border(n,first,&buf[m]);
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::unpack_border_hybrid(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++)
-    h_molecule(i) = (tagint) ubuf(buf[m++]).i;
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecAngleKokkos_PackExchangeFunctor {
   typedef DeviceType device_type;
@@ -1245,50 +802,6 @@ int AtomVecAngleKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecAngleKokkos::pack_exchange(int i, double *buf)
-{
-  int k;
-  int m = 1;
-  buf[m++] = h_x(i,0);
-  buf[m++] = h_x(i,1);
-  buf[m++] = h_x(i,2);
-  buf[m++] = h_v(i,0);
-  buf[m++] = h_v(i,1);
-  buf[m++] = h_v(i,2);
-  buf[m++] = ubuf(h_tag(i)).d;
-  buf[m++] = ubuf(h_type(i)).d;
-  buf[m++] = ubuf(h_mask(i)).d;
-  buf[m++] = ubuf(h_image(i)).d;
-  buf[m++] = ubuf(h_molecule(i)).d;
-
-  buf[m++] = ubuf(h_num_bond(i)).d;
-  for (k = 0; k < h_num_bond(i); k++) {
-    buf[m++] = ubuf(h_bond_type(i,k)).d;
-    buf[m++] = ubuf(h_bond_atom(i,k)).d;
-  }
-  buf[m++] = ubuf(h_num_angle(i)).d;
-  for (k = 0; k < h_num_angle(i); k++) {
-    buf[m++] = ubuf(h_angle_type(i,k)).d;
-    buf[m++] = ubuf(h_angle_atom1(i,k)).d;
-    buf[m++] = ubuf(h_angle_atom2(i,k)).d;
-    buf[m++] = ubuf(h_angle_atom3(i,k)).d;
-  }
-  buf[m++] = ubuf(h_nspecial(i,0)).d;
-  buf[m++] = ubuf(h_nspecial(i,1)).d;
-  buf[m++] = ubuf(h_nspecial(i,2)).d;
-  for (k = 0; k < h_nspecial(i,2); k++)
-    buf[m++] = ubuf(h_special(i,k)).d;
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecAngleKokkos_UnpackExchangeFunctor {
   typedef DeviceType device_type;
@@ -1416,361 +929,6 @@ int AtomVecAngleKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int n
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecAngleKokkos::unpack_exchange(double *buf)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) grow(0);
-  atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-           MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK |
-           ANGLE_MASK | SPECIAL_MASK);
-
-  int k;
-  int m = 1;
-  h_x(nlocal,0) = buf[m++];
-  h_x(nlocal,1) = buf[m++];
-  h_x(nlocal,2) = buf[m++];
-  h_v(nlocal,0) = buf[m++];
-  h_v(nlocal,1) = buf[m++];
-  h_v(nlocal,2) = buf[m++];
-  h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
-  h_type(nlocal) = (int) ubuf(buf[m++]).i;
-  h_mask(nlocal) = (int) ubuf(buf[m++]).i;
-  h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
-  h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
-
-  h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
-  for (k = 0; k < h_num_bond(nlocal); k++) {
-    h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
-    h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-  }
-  h_num_angle(nlocal) = (int) ubuf(buf[m++]).i;
-  for (k = 0; k < h_num_angle(nlocal); k++) {
-    h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i;
-    h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-    h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-    h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-  }
-  h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i;
-  h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i;
-  h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i;
-  for (k = 0; k < h_nspecial(nlocal,2); k++)
-   h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      m += modify->fix[atom->extra_grow[iextra]]->
-        unpack_exchange(nlocal,&buf[m]);
-
-  atom->nlocal++;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   size of restart data for all atoms owned by this proc
-   include extra data stored by fixes
-------------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::size_restart()
-{
-  int i;
-
-  int nlocal = atom->nlocal;
-  int n = 0;
-  for (i = 0; i < nlocal; i++)
-    n += 14 + 2*h_num_bond(i) + 4*h_num_angle(i);
-
-  if (atom->nextra_restart)
-    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
-      for (i = 0; i < nlocal; i++)
-        n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
-
-  return n;
-}
-
-/* ----------------------------------------------------------------------
-   pack atom I's data for restart file including extra quantities
-   xyz must be 1st 3 values, so that read_restart can test on them
-   molecular types may be negative, but write as positive
-------------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::pack_restart(int i, double *buf)
-{
-  atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-            MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK |
-            ANGLE_MASK | SPECIAL_MASK);
-
-  int m = 1;
-  buf[m++] = h_x(i,0);
-  buf[m++] = h_x(i,1);
-  buf[m++] = h_x(i,2);
-  buf[m++] = ubuf(h_tag(i)).d;
-  buf[m++] = ubuf(h_type(i)).d;
-  buf[m++] = ubuf(h_mask(i)).d;
-  buf[m++] = ubuf(h_image(i)).d;
-  buf[m++] = h_v(i,0);
-  buf[m++] = h_v(i,1);
-  buf[m++] = h_v(i,2);
-
-  buf[m++] = ubuf(h_molecule(i)).d;
-
-  buf[m++] = ubuf(h_num_bond(i)).d;
-  for (int k = 0; k < h_num_bond(i); k++) {
-    buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d;
-    buf[m++] = ubuf(h_bond_atom(i,k)).d;
-  }
-
-  buf[m++] = ubuf(h_num_angle(i)).d;
-  for (int k = 0; k < h_num_angle(i); k++) {
-    buf[m++] = ubuf(MAX(h_angle_type(i,k),-h_angle_type(i,k))).d;
-    buf[m++] = ubuf(h_angle_atom1(i,k)).d;
-    buf[m++] = ubuf(h_angle_atom2(i,k)).d;
-    buf[m++] = ubuf(h_angle_atom3(i,k)).d;
-  }
-
-  if (atom->nextra_restart)
-    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
-      m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   unpack data for one atom from restart file including extra quantities
-------------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::unpack_restart(double *buf)
-{
-  int k;
-
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) {
-    grow(0);
-    if (atom->nextra_store)
-      memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
-  }
-  atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-                MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK |
-                ANGLE_MASK | SPECIAL_MASK);
-
-  int m = 1;
-  h_x(nlocal,0) = buf[m++];
-  h_x(nlocal,1) = buf[m++];
-  h_x(nlocal,2) = buf[m++];
-  h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
-  h_type(nlocal) = (int) ubuf(buf[m++]).i;
-  h_mask(nlocal) = (int) ubuf(buf[m++]).i;
-  h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
-  h_v(nlocal,0) = buf[m++];
-  h_v(nlocal,1) = buf[m++];
-  h_v(nlocal,2) = buf[m++];
-
-  h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
-
-  h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
-  for (k = 0; k < h_num_bond(nlocal); k++) {
-    h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
-    h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-  }
-
-  h_num_angle(nlocal) = (int) ubuf(buf[m++]).i;
-  for (k = 0; k < h_num_angle(nlocal); k++) {
-    h_angle_type(nlocal,k) = (int) ubuf(buf[m++]).i;
-    h_angle_atom1(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-    h_angle_atom2(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-    h_angle_atom3(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-  }
-
-  h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
-
-  double **extra = atom->extra;
-  if (atom->nextra_store) {
-    int size = static_cast<int> (buf[0]) - m;
-    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
-  }
-
-  atom->nlocal++;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   create one atom of itype at coord
-   set other values to defaults
-------------------------------------------------------------------------- */
-
-void AtomVecAngleKokkos::create_atom(int itype, double *coord)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) {
-    atomKK->modified(Host,ALL_MASK);
-    grow(0);
-  }
-  atomKK->modified(Host,ALL_MASK);
-
-  tag[nlocal] = 0;
-  type[nlocal] = itype;
-  h_x(nlocal,0) = coord[0];
-  h_x(nlocal,1) = coord[1];
-  h_x(nlocal,2) = coord[2];
-  h_mask(nlocal) = 1;
-  h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) |
-    ((imageint) IMGMAX << IMGBITS) | IMGMAX;
-  h_v(nlocal,0) = 0.0;
-  h_v(nlocal,1) = 0.0;
-  h_v(nlocal,2) = 0.0;
-
-  h_molecule(nlocal) = 0;
-  h_num_bond(nlocal) = 0;
-  h_num_angle(nlocal) = 0;
-  h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
-
-  atom->nlocal++;
-}
-
-/* ----------------------------------------------------------------------
-   unpack one line from Atoms section of data file
-   initialize other atom quantities
-------------------------------------------------------------------------- */
-
-void AtomVecAngleKokkos::data_atom(double *coord, imageint imagetmp,
-                                  const std::vector<std::string> &values, std::string &extract)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) grow(0);
-  atomKK->modified(Host,ALL_MASK);
-
-  h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
-  h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp);
-  h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp);
-  extract = values[2];
-  if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
-    error->one(FLERR,"Invalid atom type in Atoms section of data file");
-
-  h_x(nlocal,0) = coord[0];
-  h_x(nlocal,1) = coord[1];
-  h_x(nlocal,2) = coord[2];
-
-  h_image(nlocal) = imagetmp;
-
-  h_mask(nlocal) = 1;
-  h_v(nlocal,0) = 0.0;
-  h_v(nlocal,1) = 0.0;
-  h_v(nlocal,2) = 0.0;
-  h_num_bond(nlocal) = 0;
-  h_num_angle(nlocal) = 0;
-
-  atom->nlocal++;
-}
-
-/* ----------------------------------------------------------------------
-   unpack hybrid quantities from one line in Atoms section of data file
-   initialize other atom quantities for this sub-style
-------------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
-                                         int offset)
-{
-  h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp);
-  h_num_bond(nlocal) = 0;
-  h_num_angle(nlocal) = 0;
-  return 1;
-}
-
-/* ----------------------------------------------------------------------
-   pack atom info for data file including 3 image flags
-------------------------------------------------------------------------- */
-
-void AtomVecAngleKokkos::pack_data(double **buf)
-{
-  int nlocal = atom->nlocal;
-  for (int i = 0; i < nlocal; i++) {
-    buf[i][0] = h_tag(i);
-    buf[i][1] = h_molecule(i);
-    buf[i][2] = h_type(i);
-    buf[i][3] = h_x(i,0);
-    buf[i][4] = h_x(i,1);
-    buf[i][5] = h_x(i,2);
-    buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX;
-    buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
-    buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   pack hybrid atom info for data file
-------------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::pack_data_hybrid(int i, double *buf)
-{
-  buf[0] = h_molecule(i);
-  return 1;
-}
-
-/* ----------------------------------------------------------------------
-   write atom info to data file including 3 image flags
-------------------------------------------------------------------------- */
-
-void AtomVecAngleKokkos::write_data(FILE *fp, int n, double **buf)
-{
-  for (int i = 0; i < n; i++)
-    fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
-            (int) buf[i][0],(int) buf[i][1], (int) buf[i][2],
-            buf[i][3],buf[i][4],buf[i][5],
-            (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
-}
-
-/* ----------------------------------------------------------------------
-   write hybrid atom info to data file
-------------------------------------------------------------------------- */
-
-int AtomVecAngleKokkos::write_data_hybrid(FILE *fp, double *buf)
-{
-  fprintf(fp," " TAGINT_FORMAT, (tagint) (buf[0]));
-  return 1;
-}
-
-/* ----------------------------------------------------------------------
-   return # of bytes of allocated memory
-------------------------------------------------------------------------- */
-
-double AtomVecAngleKokkos::memory_usage()
-{
-  double bytes = 0;
-
-  if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
-  if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
-  if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
-  if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
-  if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
-  if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
-  if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
-
-  if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
-  if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
-  if (atom->memcheck("special"))
-    bytes += memory->usage(special,nmax,atom->maxspecial);
-
-  if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
-  if (atom->memcheck("bond_type"))
-    bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
-  if (atom->memcheck("bond_atom"))
-    bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
-
-  if (atom->memcheck("num_angle")) bytes += memory->usage(num_angle,nmax);
-  if (atom->memcheck("angle_type"))
-    bytes += memory->usage(angle_type,nmax,atom->angle_per_atom);
-  if (atom->memcheck("angle_atom1"))
-    bytes += memory->usage(angle_atom1,nmax,atom->angle_per_atom);
-  if (atom->memcheck("angle_atom2"))
-    bytes += memory->usage(angle_atom2,nmax,atom->angle_per_atom);
-  if (atom->memcheck("angle_atom3"))
-    bytes += memory->usage(angle_atom3,nmax,atom->angle_per_atom);
-
-  return bytes;
-}
-
-/* ---------------------------------------------------------------------- */
-
 void AtomVecAngleKokkos::sync(ExecutionSpace space, unsigned int mask)
 {
   if (space == Device) {
@@ -1826,6 +984,8 @@ void AtomVecAngleKokkos::sync(ExecutionSpace space, unsigned int mask)
   }
 }
 
+/* ---------------------------------------------------------------------- */
+
 void AtomVecAngleKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int mask)
 {
   if (space == Device) {
@@ -1973,4 +1133,3 @@ void AtomVecAngleKokkos::modified(ExecutionSpace space, unsigned int mask)
     }
   }
 }
-

src/KOKKOS/atom_vec_angle_kokkos.h

@@ -24,41 +24,15 @@ AtomStyle(angle/kk/host,AtomVecAngleKokkos);
 #define LMP_ATOM_VEC_ANGLE_KOKKOS_H
 
 #include "atom_vec_kokkos.h"
+#include "atom_vec_angle.h"
 
 namespace LAMMPS_NS {
 
-class AtomVecAngleKokkos : public AtomVecKokkos {
+class AtomVecAngleKokkos : public AtomVecKokkos, public AtomVecAngle {
  public:
   AtomVecAngleKokkos(class LAMMPS *);
 
   void grow(int) override;
-  void copy(int, int, int) override;
-  int pack_comm(int, int *, double *, int, int *) override;
-  int pack_comm_vel(int, int *, double *, int, int *) override;
-  void unpack_comm(int, int, double *) override;
-  void unpack_comm_vel(int, int, double *) override;
-  int pack_reverse(int, int, double *) override;
-  void unpack_reverse(int, int *, double *) override;
-  int pack_border(int, int *, double *, int, int *) override;
-  int pack_border_vel(int, int *, double *, int, int *) override;
-  int pack_border_hybrid(int, int *, double *) override;
-  void unpack_border(int, int, double *) override;
-  void unpack_border_vel(int, int, double *) override;
-  int unpack_border_hybrid(int, int, double *) override;
-  int pack_exchange(int, double *) override;
-  int unpack_exchange(double *) override;
-  int size_restart() override;
-  int pack_restart(int, double *) override;
-  int unpack_restart(double *) override;
-  void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
-  int data_atom_hybrid(int, const std::vector<std::string> &, int) override;
-  void pack_data(double **) override;
-  int pack_data_hybrid(int, double *) override;
-  void write_data(FILE *, int, double **) override;
-  int write_data_hybrid(FILE *, double *) override;
-  double memory_usage() override;
-
   void grow_pointers() override;
   int pack_comm_kokkos(const int &n, const DAT::tdual_int_2d &k_sendlist,
                        const int & iswap,
@@ -89,21 +63,9 @@ class AtomVecAngleKokkos : public AtomVecKokkos {
   void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override;
 
  protected:
-
-  tagint *tag;
-  int *type,*mask;
-  imageint *image;
-  double **x,**v,**f;
-
   tagint *molecule;
-  int **nspecial;
   tagint **special;
-  int *num_bond;
-  int **bond_type;
   tagint **bond_atom;
-
-  int *num_angle;
-  int **angle_type;
   tagint **angle_atom1,**angle_atom2,**angle_atom3;
 
   DAT::t_tagint_1d d_tag;
@@ -142,13 +104,9 @@ class AtomVecAngleKokkos : public AtomVecKokkos {
   HAT::t_int_1d h_num_angle;
   HAT::t_int_2d h_angle_type;
   HAT::t_tagint_2d h_angle_atom1,h_angle_atom2,h_angle_atom3;
-
-  DAT::tdual_int_1d k_count;
-
 };
 
-}
+}    // namespace LAMMPS_NS
 
 #endif
 #endif
-

src/KOKKOS/atom_vec_atomic_kokkos.cpp

@@ -27,23 +27,10 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-AtomVecAtomicKokkos::AtomVecAtomicKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
+AtomVecAtomicKokkos::AtomVecAtomicKokkos(LAMMPS *lmp) : AtomVec(lmp),
+AtomVecKokkos(lmp), AtomVecAtomic(lmp)
 {
-  molecular = Atom::ATOMIC;
-  mass_type = PER_TYPE;
 
-  comm_x_only = comm_f_only = 1;
-  size_forward = 3;
-  size_reverse = 3;
-  size_border = 6;
-  size_velocity = 3;
-  size_data_atom = 5;
-  size_data_vel = 4;
-  xcol_data = 3;
-
-  k_count = DAT::tdual_int_1d("atom::k_count",1);
-  atomKK = (AtomKokkos *) atom;
-  commKK = (CommKokkos *) comm;
 }
 
 /* ----------------------------------------------------------------------
@@ -113,28 +100,6 @@ void AtomVecAtomicKokkos::grow_pointers()
   h_f = atomKK->k_f.h_view;
 }
 
-/* ----------------------------------------------------------------------
-   copy atom I info to atom J
-------------------------------------------------------------------------- */
-
-void AtomVecAtomicKokkos::copy(int i, int j, int delflag)
-{
-  h_tag[j] = h_tag[i];
-  h_type[j] = h_type[i];
-  mask[j] = mask[i];
-  h_image[j] = h_image[i];
-  h_x(j,0) = h_x(i,0);
-  h_x(j,1) = h_x(i,1);
-  h_x(j,2) = h_x(i,2);
-  h_v(j,0) = h_v(i,0);
-  h_v(j,1) = h_v(i,1);
-  h_v(j,2) = h_v(i,2);
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
-}
-
 /* ---------------------------------------------------------------------- */
 
 template<class DeviceType,int PBC_FLAG>
@@ -232,130 +197,6 @@ int AtomVecAtomicKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecAtomicKokkos::pack_border(int n, int *list, double *buf,
-                               int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0];
-      dy = pbc[1];
-      dz = pbc[2];
-    }
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0) + dx;
-      buf[m++] = h_x(j,1) + dy;
-      buf[m++] = h_x(j,2) + dz;
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-    }
-  }
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
-
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecAtomicKokkos::pack_border_vel(int n, int *list, double *buf,
-                                   int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz,dvx,dvy,dvz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = h_v(j,0);
-      buf[m++] = h_v(j,1);
-      buf[m++] = h_v(j,2);
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0];
-      dy = pbc[1];
-      dz = pbc[2];
-    }
-    if (!deform_vremap) {
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        buf[m++] = ubuf(h_tag(j)).d;
-        buf[m++] = ubuf(h_type(j)).d;
-        buf[m++] = ubuf(h_mask(j)).d;
-        buf[m++] = h_v(j,0);
-        buf[m++] = h_v(j,1);
-        buf[m++] = h_v(j,2);
-      }
-    } else {
-      dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
-      dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
-      dvz = pbc[2]*h_rate[2];
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        buf[m++] = ubuf(h_tag(j)).d;
-        buf[m++] = ubuf(h_type(j)).d;
-        buf[m++] = ubuf(h_mask(j)).d;
-        if (mask[i] & deform_groupbit) {
-          buf[m++] = h_v(j,0) + dvx;
-          buf[m++] = h_v(j,1) + dvy;
-          buf[m++] = h_v(j,2) + dvz;
-        } else {
-          buf[m++] = h_v(j,0);
-          buf[m++] = h_v(j,1);
-          buf[m++] = h_v(j,2);
-        }
-      }
-    }
-  }
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
-
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecAtomicKokkos_UnpackBorder {
   typedef DeviceType device_type;
@@ -408,63 +249,6 @@ void AtomVecAtomicKokkos::unpack_border_kokkos(const int &n, const int &first,
 
 /* ---------------------------------------------------------------------- */
 
-void AtomVecAtomicKokkos::unpack_border(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  while (last > nmax) grow(0);
-
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-    h_tag(i) =  (tagint)  ubuf(buf[m++]).i;
-    h_type(i) = (int) ubuf(buf[m++]).i;
-    h_mask(i) = (int) ubuf(buf[m++]).i;
-  }
-
-  atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK);
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->
-        unpack_border(n,first,&buf[m]);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomVecAtomicKokkos::unpack_border_vel(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  while (last > nmax) grow(0);
-
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-    h_tag(i) =  (tagint)  ubuf(buf[m++]).i;
-    h_type(i) = (int) ubuf(buf[m++]).i;
-    h_mask(i) = (int) ubuf(buf[m++]).i;
-    h_v(i,0) = buf[m++];
-    h_v(i,1) = buf[m++];
-    h_v(i,2) = buf[m++];
-  }
-
-  atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|V_MASK);
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->
-        unpack_border(n,first,&buf[m]);
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecAtomicKokkos_PackExchangeFunctor {
   typedef DeviceType device_type;
@@ -568,30 +352,6 @@ int AtomVecAtomicKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecAtomicKokkos::pack_exchange(int i, double *buf)
-{
-  int m = 1;
-  buf[m++] = h_x(i,0);
-  buf[m++] = h_x(i,1);
-  buf[m++] = h_x(i,2);
-  buf[m++] = h_v(i,0);
-  buf[m++] = h_v(i,1);
-  buf[m++] = h_v(i,2);
-  buf[m++] = ubuf(h_tag(i)).d;
-  buf[m++] = ubuf(h_type(i)).d;
-  buf[m++] = ubuf(h_mask(i)).d;
-  buf[m++] = ubuf(h_image(i)).d;
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecAtomicKokkos_UnpackExchangeFunctor {
   typedef DeviceType device_type;
@@ -671,238 +431,6 @@ int AtomVecAtomicKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecAtomicKokkos::unpack_exchange(double *buf)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) grow(0);
-  atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-           MASK_MASK | IMAGE_MASK);
-
-  int m = 1;
-  h_x(nlocal,0) = buf[m++];
-  h_x(nlocal,1) = buf[m++];
-  h_x(nlocal,2) = buf[m++];
-  h_v(nlocal,0) = buf[m++];
-  h_v(nlocal,1) = buf[m++];
-  h_v(nlocal,2) = buf[m++];
-  h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
-  h_type(nlocal) = (int) ubuf(buf[m++]).i;
-  h_mask(nlocal) = (int) ubuf(buf[m++]).i;
-  h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      m += modify->fix[atom->extra_grow[iextra]]->
-        unpack_exchange(nlocal,&buf[m]);
-
-  atom->nlocal++;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   size of restart data for all atoms owned by this proc
-   include extra data stored by fixes
-------------------------------------------------------------------------- */
-
-int AtomVecAtomicKokkos::size_restart()
-{
-  int i;
-
-  int nlocal = atom->nlocal;
-  int n = 11 * nlocal;
-
-  if (atom->nextra_restart)
-    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
-      for (i = 0; i < nlocal; i++)
-        n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
-
-  return n;
-}
-
-/* ----------------------------------------------------------------------
-   pack atom I's data for restart file including extra quantities
-   xyz must be 1st 3 values, so that read_restart can test on them
-   molecular types may be negative, but write as positive
-------------------------------------------------------------------------- */
-
-int AtomVecAtomicKokkos::pack_restart(int i, double *buf)
-{
-  atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-            MASK_MASK | IMAGE_MASK );
-
-  int m = 1;
-  buf[m++] = h_x(i,0);
-  buf[m++] = h_x(i,1);
-  buf[m++] = h_x(i,2);
-  buf[m++] = ubuf(h_tag(i)).d;
-  buf[m++] = ubuf(h_type(i)).d;
-  buf[m++] = ubuf(h_mask(i)).d;
-  buf[m++] = ubuf(h_image(i)).d;
-  buf[m++] = h_v(i,0);
-  buf[m++] = h_v(i,1);
-  buf[m++] = h_v(i,2);
-
-  if (atom->nextra_restart)
-    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
-      m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   unpack data for one atom from restart file including extra quantities
-------------------------------------------------------------------------- */
-
-int AtomVecAtomicKokkos::unpack_restart(double *buf)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) {
-    grow(0);
-    if (atom->nextra_store)
-      memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
-  }
-  atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-                MASK_MASK | IMAGE_MASK );
-
-  int m = 1;
-  h_x(nlocal,0) = buf[m++];
-  h_x(nlocal,1) = buf[m++];
-  h_x(nlocal,2) = buf[m++];
-  h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
-  h_type(nlocal) = (int) ubuf(buf[m++]).i;
-  h_mask(nlocal) = (int) ubuf(buf[m++]).i;
-  h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
-  h_v(nlocal,0) = buf[m++];
-  h_v(nlocal,1) = buf[m++];
-  h_v(nlocal,2) = buf[m++];
-
-  double **extra = atom->extra;
-  if (atom->nextra_store) {
-    int size = static_cast<int> (buf[0]) - m;
-    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
-  }
-
-  atom->nlocal++;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   create one atom of itype at coord
-   set other values to defaults
-------------------------------------------------------------------------- */
-
-void AtomVecAtomicKokkos::create_atom(int itype, double *coord)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) {
-    //if(nlocal>2) printf("typeA: %i %i\n",type[0],type[1]);
-    atomKK->modified(Host,ALL_MASK);
-    grow(0);
-    //if(nlocal>2) printf("typeB: %i %i\n",type[0],type[1]);
-  }
-  atomKK->modified(Host,ALL_MASK);
-
-  tag[nlocal] = 0;
-  type[nlocal] = itype;
-  h_x(nlocal,0) = coord[0];
-  h_x(nlocal,1) = coord[1];
-  h_x(nlocal,2) = coord[2];
-  h_mask[nlocal] = 1;
-  h_image[nlocal] = ((tagint) IMGMAX << IMG2BITS) |
-    ((tagint) IMGMAX << IMGBITS) | IMGMAX;
-  h_v(nlocal,0) = 0.0;
-  h_v(nlocal,1) = 0.0;
-  h_v(nlocal,2) = 0.0;
-
-  atom->nlocal++;
-}
-
-/* ----------------------------------------------------------------------
-   unpack one line from Atoms section of data file
-   initialize other atom quantities
-------------------------------------------------------------------------- */
-
-void AtomVecAtomicKokkos::data_atom(double *coord, imageint imagetmp,
-                                    const std::vector<std::string> &values, std::string &extract)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) grow(0);
-
-  h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp);
-  h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
-  extract = values[1];
-  if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
-    error->one(FLERR,"Invalid atom type in Atoms section of data file");
-
-  h_x(nlocal,0) = coord[0];
-  h_x(nlocal,1) = coord[1];
-  h_x(nlocal,2) = coord[2];
-
-  h_image[nlocal] = imagetmp;
-
-  h_mask[nlocal] = 1;
-  h_v(nlocal,0) = 0.0;
-  h_v(nlocal,1) = 0.0;
-  h_v(nlocal,2) = 0.0;
-
-  atomKK->modified(Host,ALL_MASK);
-
-  atom->nlocal++;
-}
-
-/* ----------------------------------------------------------------------
-   pack atom info for data file including 3 image flags
-------------------------------------------------------------------------- */
-
-void AtomVecAtomicKokkos::pack_data(double **buf)
-{
-  int nlocal = atom->nlocal;
-  for (int i = 0; i < nlocal; i++) {
-    buf[i][0] = h_tag[i];
-    buf[i][1] = h_type[i];
-    buf[i][2] = h_x(i,0);
-    buf[i][3] = h_x(i,1);
-    buf[i][4] = h_x(i,2);
-    buf[i][5] = (h_image[i] & IMGMASK) - IMGMAX;
-    buf[i][6] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
-    buf[i][7] = (h_image[i] >> IMG2BITS) - IMGMAX;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   write atom info to data file including 3 image flags
-------------------------------------------------------------------------- */
-
-void AtomVecAtomicKokkos::write_data(FILE *fp, int n, double **buf)
-{
-  for (int i = 0; i < n; i++)
-    fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
-            (int) buf[i][0],(int) buf[i][1],buf[i][2],buf[i][3],buf[i][4],
-            (int) buf[i][5],(int) buf[i][6],(int) buf[i][7]);
-}
-
-/* ----------------------------------------------------------------------
-   return # of bytes of allocated memory
-------------------------------------------------------------------------- */
-
-double AtomVecAtomicKokkos::memory_usage()
-{
-  double bytes = 0;
-
-  if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
-  if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
-  if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
-  if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
-  if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
-  if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
-  if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
-
-  return bytes;
-}
-
-/* ---------------------------------------------------------------------- */
-
 void AtomVecAtomicKokkos::sync(ExecutionSpace space, unsigned int mask)
 {
   if (space == Device) {
@@ -983,4 +511,3 @@ void AtomVecAtomicKokkos::modified(ExecutionSpace space, unsigned int mask)
     if (mask & IMAGE_MASK) atomKK->k_image.modify<LMPHostType>();
   }
 }
-

src/KOKKOS/atom_vec_atomic_kokkos.h

@@ -24,31 +24,16 @@ AtomStyle(atomic/kk/host,AtomVecAtomicKokkos);
 #define LMP_ATOM_VEC_ATOMIC_KOKKOS_H
 
 #include "atom_vec_kokkos.h"
+#include "atom_vec_atomic.h"
 #include "kokkos_type.h"
 
 namespace LAMMPS_NS {
 
-class AtomVecAtomicKokkos : public AtomVecKokkos {
+class AtomVecAtomicKokkos : public AtomVecKokkos, public AtomVecAtomic {
  public:
   AtomVecAtomicKokkos(class LAMMPS *);
 
   void grow(int) override;
-  void copy(int, int, int) override;
-  int pack_border(int, int *, double *, int, int *) override;
-  int pack_border_vel(int, int *, double *, int, int *) override;
-  void unpack_border(int, int, double *) override;
-  void unpack_border_vel(int, int, double *) override;
-  int pack_exchange(int, double *) override;
-  int unpack_exchange(double *) override;
-  int size_restart() override;
-  int pack_restart(int, double *) override;
-  int unpack_restart(double *) override;
-  void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
-  void pack_data(double **) override;
-  void write_data(FILE *, int, double **) override;
-  double memory_usage() override;
-
   void grow_pointers() override;
   int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
                          DAT::tdual_xfloat_2d buf,int iswap,
@@ -70,11 +55,6 @@ class AtomVecAtomicKokkos : public AtomVecKokkos {
   void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override;
 
  protected:
-  tagint *tag;
-  imageint *image;
-  int *type,*mask;
-  double **x,**v,**f;
-
   DAT::t_tagint_1d d_tag;
   HAT::t_tagint_1d h_tag;
   DAT::t_imageint_1d d_image;
@@ -85,8 +65,6 @@ class AtomVecAtomicKokkos : public AtomVecKokkos {
   DAT::t_x_array d_x;
   DAT::t_v_array d_v;
   DAT::t_f_array d_f;
-
-  DAT::tdual_int_1d k_count;
 };
 
 }

src/KOKKOS/atom_vec_bond_kokkos.cpp

@@ -27,26 +27,10 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-AtomVecBondKokkos::AtomVecBondKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
+AtomVecBondKokkos::AtomVecBondKokkos(LAMMPS *lmp) : AtomVec(lmp),
+AtomVecKokkos(lmp), AtomVecBond(lmp)
 {
-  molecular = Atom::MOLECULAR;
-  bonds_allow = 1;
-  mass_type = PER_TYPE;
 
-  comm_x_only = comm_f_only = 1;
-  size_forward = 3;
-  size_reverse = 3;
-  size_border = 7;
-  size_velocity = 3;
-  size_data_atom = 6;
-  size_data_vel = 4;
-  xcol_data = 4;
-
-  atom->molecule_flag = 1;
-
-  k_count = DAT::tdual_int_1d("atom::k_count",1);
-  atomKK = (AtomKokkos *) atom;
-  commKK = (CommKokkos *) comm;
 }
 
 /* ----------------------------------------------------------------------
@@ -142,43 +126,6 @@ void AtomVecBondKokkos::grow_pointers()
   h_bond_atom = atomKK->k_bond_atom.h_view;
 }
 
-/* ----------------------------------------------------------------------
-   copy atom I info to atom J
-------------------------------------------------------------------------- */
-
-void AtomVecBondKokkos::copy(int i, int j, int delflag)
-{
-  int k;
-
-  h_tag[j] = h_tag[i];
-  h_type[j] = h_type[i];
-  mask[j] = mask[i];
-  h_image[j] = h_image[i];
-  h_x(j,0) = h_x(i,0);
-  h_x(j,1) = h_x(i,1);
-  h_x(j,2) = h_x(i,2);
-  h_v(j,0) = h_v(i,0);
-  h_v(j,1) = h_v(i,1);
-  h_v(j,2) = h_v(i,2);
-
-  h_molecule(j) = h_molecule(i);
-
-  h_num_bond(j) = h_num_bond(i);
-  for (k = 0; k < h_num_bond(j); k++) {
-    h_bond_type(j,k) = h_bond_type(i,k);
-    h_bond_atom(j,k) = h_bond_atom(i,k);
-  }
-
-  h_nspecial(j,0) = h_nspecial(i,0);
-  h_nspecial(j,1) = h_nspecial(i,1);
-  h_nspecial(j,2) = h_nspecial(i,2);
-  for (k = 0; k < h_nspecial(j,2); k++) h_special(j,k) = h_special(i,k);
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
-}
-
 /* ---------------------------------------------------------------------- */
 
 template<class DeviceType,int PBC_FLAG>
@@ -282,149 +229,6 @@ int AtomVecBondKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecBondKokkos::pack_border(int n, int *list, double *buf,
-                                   int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = ubuf(h_molecule(j)).d;
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0];
-      dy = pbc[1];
-      dz = pbc[2];
-    }
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0) + dx;
-      buf[m++] = h_x(j,1) + dy;
-      buf[m++] = h_x(j,2) + dz;
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = ubuf(h_molecule(j)).d;
-    }
-  }
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
-
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecBondKokkos::pack_border_vel(int n, int *list, double *buf,
-                                       int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz,dvx,dvy,dvz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = ubuf(h_molecule(j)).d;
-      buf[m++] = h_v(j,0);
-      buf[m++] = h_v(j,1);
-      buf[m++] = h_v(j,2);
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0];
-      dy = pbc[1];
-      dz = pbc[2];
-    }
-    if (!deform_vremap) {
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        buf[m++] = ubuf(h_tag(j)).d;
-        buf[m++] = ubuf(h_type(j)).d;
-        buf[m++] = ubuf(h_mask(j)).d;
-        buf[m++] = ubuf(h_molecule(j)).d;
-        buf[m++] = h_v(j,0);
-        buf[m++] = h_v(j,1);
-        buf[m++] = h_v(j,2);
-      }
-    } else {
-      dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
-      dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
-      dvz = pbc[2]*h_rate[2];
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        buf[m++] = ubuf(h_tag(j)).d;
-        buf[m++] = ubuf(h_type(j)).d;
-        buf[m++] = ubuf(h_mask(j)).d;
-        buf[m++] = ubuf(h_molecule(j)).d;
-        if (mask[i] & deform_groupbit) {
-          buf[m++] = h_v(j,0) + dvx;
-          buf[m++] = h_v(j,1) + dvy;
-          buf[m++] = h_v(j,2) + dvz;
-        } else {
-          buf[m++] = h_v(j,0);
-          buf[m++] = h_v(j,1);
-          buf[m++] = h_v(j,2);
-        }
-      }
-    }
-  }
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
-
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecBondKokkos::pack_border_hybrid(int n, int *list, double *buf)
-{
-  int i,j,m;
-
-  m = 0;
-  for (i = 0; i < n; i++) {
-    j = list[i];
-    buf[m++] = h_molecule(j);
-  }
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecBondKokkos_UnpackBorder {
   typedef DeviceType device_type;
@@ -485,78 +289,6 @@ void AtomVecBondKokkos::unpack_border_kokkos(const int &n, const int &first,
 
 /* ---------------------------------------------------------------------- */
 
-void AtomVecBondKokkos::unpack_border(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  while (last > nmax) grow(0);
-
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-    h_tag(i) =  (tagint)  ubuf(buf[m++]).i;
-    h_type(i) = (int) ubuf(buf[m++]).i;
-    h_mask(i) = (int) ubuf(buf[m++]).i;
-    h_molecule(i) = (tagint) ubuf(buf[m++]).i;
-  }
-
-  atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK);
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->
-        unpack_border(n,first,&buf[m]);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomVecBondKokkos::unpack_border_vel(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  while (last > nmax) grow(0);
-
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-    h_tag(i) =  (tagint)  ubuf(buf[m++]).i;
-    h_type(i) = (int) ubuf(buf[m++]).i;
-    h_mask(i) = (int) ubuf(buf[m++]).i;
-    h_molecule(i) = (tagint) ubuf(buf[m++]).i;
-    h_v(i,0) = buf[m++];
-    h_v(i,1) = buf[m++];
-    h_v(i,2) = buf[m++];
-  }
-
-  atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|V_MASK);
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->
-        unpack_border(n,first,&buf[m]);
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecBondKokkos::unpack_border_hybrid(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++)
-    h_molecule(i) = (tagint) ubuf(buf[m++]).i;
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecBondKokkos_PackExchangeFunctor {
   typedef DeviceType device_type;
@@ -721,43 +453,6 @@ int AtomVecBondKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecBondKokkos::pack_exchange(int i, double *buf)
-{
-  int k;
-  int m = 1;
-  buf[m++] = h_x(i,0);
-  buf[m++] = h_x(i,1);
-  buf[m++] = h_x(i,2);
-  buf[m++] = h_v(i,0);
-  buf[m++] = h_v(i,1);
-  buf[m++] = h_v(i,2);
-  buf[m++] = ubuf(h_tag(i)).d;
-  buf[m++] = ubuf(h_type(i)).d;
-  buf[m++] = ubuf(h_mask(i)).d;
-  buf[m++] = ubuf(h_image(i)).d;
-  buf[m++] = ubuf(h_molecule(i)).d;
-
-  buf[m++] = ubuf(h_num_bond(i)).d;
-  for (k = 0; k < h_num_bond(i); k++) {
-    buf[m++] = ubuf(h_bond_type(i,k)).d;
-    buf[m++] = ubuf(h_bond_atom(i,k)).d;
-  }
-  buf[m++] = ubuf(h_nspecial(i,0)).d;
-  buf[m++] = ubuf(h_nspecial(i,1)).d;
-  buf[m++] = ubuf(h_nspecial(i,2)).d;
-  for (k = 0; k < h_nspecial(i,2); k++)
-    buf[m++] = ubuf(h_special(i,k)).d;
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecBondKokkos_UnpackExchangeFunctor {
   typedef DeviceType device_type;
@@ -870,321 +565,6 @@ int AtomVecBondKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nr
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecBondKokkos::unpack_exchange(double *buf)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) grow(0);
-  atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-           MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | SPECIAL_MASK);
-
-  int k;
-  int m = 1;
-  h_x(nlocal,0) = buf[m++];
-  h_x(nlocal,1) = buf[m++];
-  h_x(nlocal,2) = buf[m++];
-  h_v(nlocal,0) = buf[m++];
-  h_v(nlocal,1) = buf[m++];
-  h_v(nlocal,2) = buf[m++];
-  h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
-  h_type(nlocal) = (int) ubuf(buf[m++]).i;
-  h_mask(nlocal) = (int) ubuf(buf[m++]).i;
-  h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
-  h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
-
-  h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
-  for (k = 0; k < h_num_bond(nlocal); k++) {
-    h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
-    h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-  }
-
-  h_nspecial(nlocal,0) = (int) ubuf(buf[m++]).i;
-  h_nspecial(nlocal,1) = (int) ubuf(buf[m++]).i;
-  h_nspecial(nlocal,2) = (int) ubuf(buf[m++]).i;
-  for (k = 0; k < h_nspecial(nlocal,2); k++)
-   h_special(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      m += modify->fix[atom->extra_grow[iextra]]->
-        unpack_exchange(nlocal,&buf[m]);
-
-  atom->nlocal++;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   size of restart data for all atoms owned by this proc
-   include extra data stored by fixes
-------------------------------------------------------------------------- */
-
-int AtomVecBondKokkos::size_restart()
-{
-  int i;
-
-  int nlocal = atom->nlocal;
-  int n = 0;
-  for (i = 0; i < nlocal; i++)
-    n += 13 + 2*h_num_bond[i];
-
-  if (atom->nextra_restart)
-    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
-      for (i = 0; i < nlocal; i++)
-        n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
-
-  return n;
-}
-
-/* ----------------------------------------------------------------------
-   pack atom I's data for restart file including extra quantities
-   xyz must be 1st 3 values, so that read_restart can test on them
-   molecular types may be negative, but write as positive
-------------------------------------------------------------------------- */
-
-int AtomVecBondKokkos::pack_restart(int i, double *buf)
-{
-  atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-            MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | SPECIAL_MASK);
-  int m = 1;
-  buf[m++] = h_x(i,0);
-  buf[m++] = h_x(i,1);
-  buf[m++] = h_x(i,2);
-  buf[m++] = ubuf(h_tag(i)).d;
-  buf[m++] = ubuf(h_type(i)).d;
-  buf[m++] = ubuf(h_mask(i)).d;
-  buf[m++] = ubuf(h_image(i)).d;
-  buf[m++] = h_v(i,0);
-  buf[m++] = h_v(i,1);
-  buf[m++] = h_v(i,2);
-
-  buf[m++] = ubuf(h_molecule(i)).d;
-
-  buf[m++] = ubuf(h_num_bond(i)).d;
-  for (int k = 0; k < h_num_bond(i); k++) {
-    buf[m++] = ubuf(MAX(h_bond_type(i,k),-h_bond_type(i,k))).d;
-    buf[m++] = ubuf(h_bond_atom(i,k)).d;
-  }
-
-  if (atom->nextra_restart)
-    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
-      m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   unpack data for one atom from restart file including extra quantities
-------------------------------------------------------------------------- */
-
-int AtomVecBondKokkos::unpack_restart(double *buf)
-{
-  int k;
-
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) {
-    grow(0);
-    if (atom->nextra_store)
-      memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
-  }
-  atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-           MASK_MASK | IMAGE_MASK | MOLECULE_MASK | BOND_MASK | SPECIAL_MASK);
-  int m = 1;
-  h_x(nlocal,0) = buf[m++];
-  h_x(nlocal,1) = buf[m++];
-  h_x(nlocal,2) = buf[m++];
-  h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
-  h_type(nlocal) = (int) ubuf(buf[m++]).i;
-  h_mask(nlocal) = (int) ubuf(buf[m++]).i;
-  h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
-  h_v(nlocal,0) = buf[m++];
-  h_v(nlocal,1) = buf[m++];
-  h_v(nlocal,2) = buf[m++];
-
-  h_molecule(nlocal) = (tagint) ubuf(buf[m++]).i;
-
-  h_num_bond(nlocal) = (int) ubuf(buf[m++]).i;
-  for (k = 0; k < h_num_bond(nlocal); k++) {
-    h_bond_type(nlocal,k) = (int) ubuf(buf[m++]).i;
-    h_bond_atom(nlocal,k) = (tagint) ubuf(buf[m++]).i;
-  }
-
-  h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
-
-  double **extra = atom->extra;
-  if (atom->nextra_store) {
-    int size = static_cast<int> (buf[0]) - m;
-    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
-  }
-
-  atom->nlocal++;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   create one atom of itype at coord
-   set other values to defaults
-------------------------------------------------------------------------- */
-
-void AtomVecBondKokkos::create_atom(int itype, double *coord)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) {
-    atomKK->modified(Host,ALL_MASK);
-    grow(0);
-  }
-  atomKK->modified(Host,ALL_MASK);
-
-  tag[nlocal] = 0;
-  type[nlocal] = itype;
-  h_x(nlocal,0) = coord[0];
-  h_x(nlocal,1) = coord[1];
-  h_x(nlocal,2) = coord[2];
-  h_mask(nlocal) = 1;
-  h_image(nlocal) = ((imageint) IMGMAX << IMG2BITS) |
-    ((imageint) IMGMAX << IMGBITS) | IMGMAX;
-  h_v(nlocal,0) = 0.0;
-  h_v(nlocal,1) = 0.0;
-  h_v(nlocal,2) = 0.0;
-
-  h_molecule(nlocal) = 0;
-  h_num_bond(nlocal) = 0;
-  h_nspecial(nlocal,0) = h_nspecial(nlocal,1) = h_nspecial(nlocal,2) = 0;
-
-  atom->nlocal++;
-}
-
-/* ----------------------------------------------------------------------
-   unpack one line from Atoms section of data file
-   initialize other atom quantities
-------------------------------------------------------------------------- */
-
-void AtomVecBondKokkos::data_atom(double *coord, imageint imagetmp,
-                                  const std::vector<std::string> &values, std::string &extract)
-{
-  int nlocal = atomKK->nlocal;
-  if (nlocal == nmax) grow(0);
-  atomKK->modified(Host,ALL_MASK);
-
-  h_tag(nlocal) = utils::inumeric(FLERR,values[0],true,lmp);
-  h_molecule(nlocal) = utils::inumeric(FLERR,values[1],true,lmp);
-  h_type(nlocal) = utils::inumeric(FLERR,values[2],true,lmp);
-  extract = values[2];
-  if (h_type(nlocal) <= 0 || h_type(nlocal) > atom->ntypes)
-    error->one(FLERR,"Invalid atom type in Atoms section of data file");
-
-  h_x(nlocal,0) = coord[0];
-  h_x(nlocal,1) = coord[1];
-  h_x(nlocal,2) = coord[2];
-
-  h_image(nlocal) = imagetmp;
-
-  h_mask(nlocal) = 1;
-  h_v(nlocal,0) = 0.0;
-  h_v(nlocal,1) = 0.0;
-  h_v(nlocal,2) = 0.0;
-  h_num_bond(nlocal) = 0;
-
-  atomKK->nlocal++;
-}
-
-/* ----------------------------------------------------------------------
-   unpack hybrid quantities from one line in Atoms section of data file
-   initialize other atom quantities for this sub-style
-------------------------------------------------------------------------- */
-
-int AtomVecBondKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
-                                        int offset)
-{
-  h_molecule(nlocal) = utils::inumeric(FLERR,values[offset],true,lmp);
-  h_num_bond(nlocal) = 0;
-  return 1;
-}
-
-/* ----------------------------------------------------------------------
-   pack atom info for data file including 3 image flags
-------------------------------------------------------------------------- */
-
-void AtomVecBondKokkos::pack_data(double **buf)
-{
-  int nlocal = atom->nlocal;
-  for (int i = 0; i < nlocal; i++) {
-    buf[i][0] = h_tag(i);
-    buf[i][1] = h_molecule(i);
-    buf[i][2] = h_type(i);
-    buf[i][3] = h_x(i,0);
-    buf[i][4] = h_x(i,1);
-    buf[i][5] = h_x(i,2);
-    buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX;
-    buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
-    buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   pack hybrid atom info for data file
-------------------------------------------------------------------------- */
-
-int AtomVecBondKokkos::pack_data_hybrid(int i, double *buf)
-{
-  buf[0] = h_molecule(i);
-  return 1;
-}
-
-/* ----------------------------------------------------------------------
-   write atom info to data file including 3 image flags
-------------------------------------------------------------------------- */
-
-void AtomVecBondKokkos::write_data(FILE *fp, int n, double **buf)
-{
-  for (int i = 0; i < n; i++)
-    fprintf(fp,"%d %d %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
-            (int) buf[i][0],(int) buf[i][1], (int) buf[i][2],
-            buf[i][3],buf[i][4],buf[i][5],
-            (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
-}
-
-/* ----------------------------------------------------------------------
-   write hybrid atom info to data file
-------------------------------------------------------------------------- */
-
-int AtomVecBondKokkos::write_data_hybrid(FILE *fp, double *buf)
-{
-  fprintf(fp," " TAGINT_FORMAT, (tagint) (buf[0]));
-  return 1;
-}
-
-/* ----------------------------------------------------------------------
-   return # of bytes of allocated memory
-------------------------------------------------------------------------- */
-
-double AtomVecBondKokkos::memory_usage()
-{
-  double bytes = 0;
-
-  if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
-  if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
-  if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
-  if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
-  if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
-  if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
-  if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
-
-  if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
-  if (atom->memcheck("nspecial")) bytes += memory->usage(nspecial,nmax,3);
-  if (atom->memcheck("special"))
-    bytes += memory->usage(special,nmax,atom->maxspecial);
-
-  if (atom->memcheck("num_bond")) bytes += memory->usage(num_bond,nmax);
-  if (atom->memcheck("bond_type"))
-    bytes += memory->usage(bond_type,nmax,atom->bond_per_atom);
-  if (atom->memcheck("bond_atom"))
-    bytes += memory->usage(bond_atom,nmax,atom->bond_per_atom);
-
-  return bytes;
-}
-
-/* ---------------------------------------------------------------------- */
-
 void AtomVecBondKokkos::sync(ExecutionSpace space, unsigned int mask)
 {
   if (space == Device) {
@@ -1337,4 +717,3 @@ void AtomVecBondKokkos::modified(ExecutionSpace space, unsigned int mask)
     }
   }
 }
-

src/KOKKOS/atom_vec_bond_kokkos.h

@@ -24,35 +24,15 @@ AtomStyle(bond/kk/host,AtomVecBondKokkos);
 #define LMP_ATOM_VEC_BOND_KOKKOS_H
 
 #include "atom_vec_kokkos.h"
+#include "atom_vec_bond.h"
 
 namespace LAMMPS_NS {
 
-class AtomVecBondKokkos : public AtomVecKokkos {
+class AtomVecBondKokkos : public AtomVecKokkos, public AtomVecBond {
  public:
   AtomVecBondKokkos(class LAMMPS *);
 
   void grow(int) override;
-  void copy(int, int, int) override;
-  int pack_border(int, int *, double *, int, int *) override;
-  int pack_border_vel(int, int *, double *, int, int *) override;
-  int pack_border_hybrid(int, int *, double *) override;
-  void unpack_border(int, int, double *) override;
-  void unpack_border_vel(int, int, double *) override;
-  int unpack_border_hybrid(int, int, double *) override;
-  int pack_exchange(int, double *) override;
-  int unpack_exchange(double *) override;
-  int size_restart() override;
-  int pack_restart(int, double *) override;
-  int unpack_restart(double *) override;
-  void create_atom(int, double *) override;
-  void data_atom(double *, imageint, const std::vector<std::string> &, std::string &) override;
-  int data_atom_hybrid(int, const std::vector<std::string> &, int) override;
-  void pack_data(double **) override;
-  int pack_data_hybrid(int, double *) override;
-  void write_data(FILE *, int, double **) override;
-  int write_data_hybrid(FILE *, double *) override;
-  double memory_usage() override;
-
   void grow_pointers() override;
   int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
                          DAT::tdual_xfloat_2d buf,int iswap,
@@ -73,18 +53,9 @@ class AtomVecBondKokkos : public AtomVecKokkos {
   void modified(ExecutionSpace space, unsigned int mask) override;
   void sync_overlapping_device(ExecutionSpace space, unsigned int mask) override;
 
- protected:
+ private:
-
-  tagint *tag;
-  int *type,*mask;
-  imageint *image;
-  double **x,**v,**f;
-
   tagint *molecule;
-  int **nspecial;
   tagint **special;
-  int *num_bond;
-  int **bond_type;
   tagint **bond_atom;
 
   DAT::t_tagint_1d d_tag;
@@ -112,9 +83,6 @@ class AtomVecBondKokkos : public AtomVecKokkos {
   HAT::t_int_1d h_num_bond;
   HAT::t_int_2d h_bond_type;
   HAT::t_tagint_2d h_bond_atom;
-
-  DAT::tdual_int_1d k_count;
-
 };
 
 }

src/KOKKOS/atom_vec_charge_kokkos.cpp

@@ -27,25 +27,9 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-AtomVecChargeKokkos::AtomVecChargeKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp)
+AtomVecChargeKokkos::AtomVecChargeKokkos(LAMMPS *lmp) : AtomVec(lmp),
+AtomVecKokkos(lmp), AtomVecCharge(lmp)
 {
-  molecular = Atom::ATOMIC;
-  mass_type = PER_TYPE;
-
-  comm_x_only = comm_f_only = 1;
-  size_forward = 3;
-  size_reverse = 3;
-  size_border = 7;
-  size_velocity = 3;
-  size_data_atom = 6;
-  size_data_vel = 4;
-  xcol_data = 4;
-
-  atom->q_flag = 1;
-
-  k_count = DAT::tdual_int_1d("atom::k_count",1);
-  atomKK = (AtomKokkos *) atom;
-  commKK = (CommKokkos *) comm;
 
 }
 
@@ -123,30 +107,6 @@ void AtomVecChargeKokkos::grow_pointers()
 
 }
 
-/* ----------------------------------------------------------------------
-   copy atom I info to atom J
-------------------------------------------------------------------------- */
-
-void AtomVecChargeKokkos::copy(int i, int j, int delflag)
-{
-  h_tag[j] = h_tag[i];
-  h_type[j] = h_type[i];
-  mask[j] = mask[i];
-  h_image[j] = h_image[i];
-  h_x(j,0) = h_x(i,0);
-  h_x(j,1) = h_x(i,1);
-  h_x(j,2) = h_x(i,2);
-  h_v(j,0) = h_v(i,0);
-  h_v(j,1) = h_v(i,1);
-  h_v(j,2) = h_v(i,2);
-
-  h_q[j] = h_q[i];
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
-}
-
 /* ---------------------------------------------------------------------- */
 
 template<class DeviceType,int PBC_FLAG,int TRICLINIC>
@@ -297,150 +257,6 @@ int AtomVecChargeKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
   return n*size_border;
 }
 
-/* ---------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::pack_border(int n, int *list, double *buf,
-                               int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = h_q(j);
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0];
-      dy = pbc[1];
-      dz = pbc[2];
-    }
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0) + dx;
-      buf[m++] = h_x(j,1) + dy;
-      buf[m++] = h_x(j,2) + dz;
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = h_q(j);
-    }
-  }
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
-
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::pack_border_vel(int n, int *list, double *buf,
-                                   int pbc_flag, int *pbc)
-{
-  int i,j,m;
-  double dx,dy,dz,dvx,dvy,dvz;
-
-  m = 0;
-  if (pbc_flag == 0) {
-    for (i = 0; i < n; i++) {
-      j = list[i];
-      buf[m++] = h_x(j,0);
-      buf[m++] = h_x(j,1);
-      buf[m++] = h_x(j,2);
-      buf[m++] = ubuf(h_tag(j)).d;
-      buf[m++] = ubuf(h_type(j)).d;
-      buf[m++] = ubuf(h_mask(j)).d;
-      buf[m++] = h_q[j];
-      buf[m++] = h_v(j,0);
-      buf[m++] = h_v(j,1);
-      buf[m++] = h_v(j,2);
-    }
-  } else {
-    if (domain->triclinic == 0) {
-      dx = pbc[0]*domain->xprd;
-      dy = pbc[1]*domain->yprd;
-      dz = pbc[2]*domain->zprd;
-    } else {
-      dx = pbc[0];
-      dy = pbc[1];
-      dz = pbc[2];
-    }
-    if (!deform_vremap) {
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        buf[m++] = ubuf(h_tag(j)).d;
-        buf[m++] = ubuf(h_type(j)).d;
-        buf[m++] = ubuf(h_mask(j)).d;
-        buf[m++] = h_q[j];
-        buf[m++] = h_v(j,0);
-        buf[m++] = h_v(j,1);
-        buf[m++] = h_v(j,2);
-      }
-    } else {
-      dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
-      dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
-      dvz = pbc[2]*h_rate[2];
-      for (i = 0; i < n; i++) {
-        j = list[i];
-        buf[m++] = h_x(j,0) + dx;
-        buf[m++] = h_x(j,1) + dy;
-        buf[m++] = h_x(j,2) + dz;
-        buf[m++] = ubuf(h_tag(j)).d;
-        buf[m++] = ubuf(h_type(j)).d;
-        buf[m++] = ubuf(h_mask(j)).d;
-        buf[m++] = h_q[j];
-        if (mask[i] & deform_groupbit) {
-          buf[m++] = h_v(j,0) + dvx;
-          buf[m++] = h_v(j,1) + dvy;
-          buf[m++] = h_v(j,2) + dvz;
-        } else {
-          buf[m++] = h_v(j,0);
-          buf[m++] = h_v(j,1);
-          buf[m++] = h_v(j,2);
-        }
-      }
-    }
-  }
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
-
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::pack_border_hybrid(int n, int *list, double *buf)
-{
-  int i,j,m;
-
-  m = 0;
-  for (i = 0; i < n; i++) {
-    j = list[i];
-    buf[m++] = h_q[j];
-  }
-  return m;
-}
-
-
 /* ---------------------------------------------------------------------- */
 
 template<class DeviceType>
@@ -500,78 +316,6 @@ void AtomVecChargeKokkos::unpack_border_kokkos(const int &n, const int &first,
 
 /* ---------------------------------------------------------------------- */
 
-void AtomVecChargeKokkos::unpack_border(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  while (last > nmax) grow(0);
-
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-    h_tag(i) =  (tagint)  ubuf(buf[m++]).i;
-    h_type(i) = (int) ubuf(buf[m++]).i;
-    h_mask(i) = (int) ubuf(buf[m++]).i;
-    h_q[i] = buf[m++];
-  }
-
-  atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK);
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->
-        unpack_border(n,first,&buf[m]);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void AtomVecChargeKokkos::unpack_border_vel(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  while (last > nmax) grow(0);
-
-  for (i = first; i < last; i++) {
-    h_x(i,0) = buf[m++];
-    h_x(i,1) = buf[m++];
-    h_x(i,2) = buf[m++];
-    h_tag(i) =  (tagint)  ubuf(buf[m++]).i;
-    h_type(i) = (int) ubuf(buf[m++]).i;
-    h_mask(i) = (int) ubuf(buf[m++]).i;
-    h_q[i] = buf[m++];
-    h_v(i,0) = buf[m++];
-    h_v(i,1) = buf[m++];
-    h_v(i,2) = buf[m++];
-  }
-
-  atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|Q_MASK|V_MASK);
-
-  if (atom->nextra_border)
-    for (int iextra = 0; iextra < atom->nextra_border; iextra++)
-      m += modify->fix[atom->extra_border[iextra]]->
-        unpack_border(n,first,&buf[m]);
-}
-
-/* ---------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::unpack_border_hybrid(int n, int first, double *buf)
-{
-  int i,m,last;
-
-  m = 0;
-  last = first + n;
-  for (i = first; i < last; i++)
-    h_q[i] = buf[m++];
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecChargeKokkos_PackExchangeFunctor {
   typedef DeviceType device_type;
@@ -688,31 +432,6 @@ int AtomVecChargeKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecChargeKokkos::pack_exchange(int i, double *buf)
-{
-  int m = 1;
-  buf[m++] = h_x(i,0);
-  buf[m++] = h_x(i,1);
-  buf[m++] = h_x(i,2);
-  buf[m++] = h_v(i,0);
-  buf[m++] = h_v(i,1);
-  buf[m++] = h_v(i,2);
-  buf[m++] = ubuf(h_tag(i)).d;
-  buf[m++] = ubuf(h_type(i)).d;
-  buf[m++] = ubuf(h_mask(i)).d;
-  buf[m++] = ubuf(h_image(i)).d;
-  buf[m++] = h_q[i];
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ---------------------------------------------------------------------- */
-
 template<class DeviceType>
 struct AtomVecChargeKokkos_UnpackExchangeFunctor {
   typedef DeviceType device_type;
@@ -797,281 +516,6 @@ int AtomVecChargeKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int
 
 /* ---------------------------------------------------------------------- */
 
-int AtomVecChargeKokkos::unpack_exchange(double *buf)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) grow(0);
-  atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-           MASK_MASK | IMAGE_MASK | Q_MASK);
-
-  int m = 1;
-  h_x(nlocal,0) = buf[m++];
-  h_x(nlocal,1) = buf[m++];
-  h_x(nlocal,2) = buf[m++];
-  h_v(nlocal,0) = buf[m++];
-  h_v(nlocal,1) = buf[m++];
-  h_v(nlocal,2) = buf[m++];
-  h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
-  h_type(nlocal) = (int) ubuf(buf[m++]).i;
-  h_mask(nlocal) = (int) ubuf(buf[m++]).i;
-  h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
-  h_q[nlocal] = buf[m++];
-
-  if (atom->nextra_grow)
-    for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
-      m += modify->fix[atom->extra_grow[iextra]]->
-        unpack_exchange(nlocal,&buf[m]);
-
-  atom->nlocal++;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   size of restart data for all atoms owned by this proc
-   include extra data stored by fixes
-------------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::size_restart()
-{
-  int i;
-
-  int nlocal = atom->nlocal;
-  int n = 12 * nlocal;
-
-  if (atom->nextra_restart)
-    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
-      for (i = 0; i < nlocal; i++)
-        n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
-
-  return n;
-}
-
-/* ----------------------------------------------------------------------
-   pack atom I's data for restart file including extra quantities
-   xyz must be 1st 3 values, so that read_restart can test on them
-   molecular types may be negative, but write as positive
-------------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::pack_restart(int i, double *buf)
-{
-  atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-            MASK_MASK | IMAGE_MASK | Q_MASK);
-
-  int m = 1;
-  buf[m++] = h_x(i,0);
-  buf[m++] = h_x(i,1);
-  buf[m++] = h_x(i,2);
-  buf[m++] = ubuf(h_tag(i)).d;
-  buf[m++] = ubuf(h_type(i)).d;
-  buf[m++] = ubuf(h_mask(i)).d;
-  buf[m++] = ubuf(h_image(i)).d;
-  buf[m++] = h_v(i,0);
-  buf[m++] = h_v(i,1);
-  buf[m++] = h_v(i,2);
-
-  buf[m++] = h_q[i];
-
-  if (atom->nextra_restart)
-    for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
-      m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
-
-  buf[0] = m;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   unpack data for one atom from restart file including extra quantities
-------------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::unpack_restart(double *buf)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) {
-    grow(0);
-    if (atom->nextra_store)
-      memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
-  }
-
-  atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK |
-           MASK_MASK | IMAGE_MASK | Q_MASK);
-
-  int m = 1;
-  h_x(nlocal,0) = buf[m++];
-  h_x(nlocal,1) = buf[m++];
-  h_x(nlocal,2) = buf[m++];
-  h_tag(nlocal) = (tagint) ubuf(buf[m++]).i;
-  h_type(nlocal) = (int) ubuf(buf[m++]).i;
-  h_mask(nlocal) = (int) ubuf(buf[m++]).i;
-  h_image(nlocal) = (imageint) ubuf(buf[m++]).i;
-  h_v(nlocal,0) = buf[m++];
-  h_v(nlocal,1) = buf[m++];
-  h_v(nlocal,2) = buf[m++];
-
-  h_q[nlocal] = buf[m++];
-
-  double **extra = atom->extra;
-  if (atom->nextra_store) {
-    int size = static_cast<int> (buf[0]) - m;
-    for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
-  }
-
-  atom->nlocal++;
-  return m;
-}
-
-/* ----------------------------------------------------------------------
-   create one atom of itype at coord
-   set other values to defaults
-------------------------------------------------------------------------- */
-
-void AtomVecChargeKokkos::create_atom(int itype, double *coord)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) {
-    atomKK->modified(Host,ALL_MASK);
-    grow(0);
-  }
-  atomKK->sync(Host,ALL_MASK);
-  atomKK->modified(Host,ALL_MASK);
-
-  tag[nlocal] = 0;
-  type[nlocal] = itype;
-  h_x(nlocal,0) = coord[0];
-  h_x(nlocal,1) = coord[1];
-  h_x(nlocal,2) = coord[2];
-  h_mask[nlocal] = 1;
-  h_image[nlocal] = ((imageint) IMGMAX << IMG2BITS) |
-    ((imageint) IMGMAX << IMGBITS) | IMGMAX;
-  h_v(nlocal,0) = 0.0;
-  h_v(nlocal,1) = 0.0;
-  h_v(nlocal,2) = 0.0;
-
-  h_q[nlocal] = 0.0;
-
-  atom->nlocal++;
-}
-
-/* ----------------------------------------------------------------------
-   unpack one line from Atoms section of data file
-   initialize other atom quantities
-------------------------------------------------------------------------- */
-
-void AtomVecChargeKokkos::data_atom(double *coord, imageint imagetmp,
-                                    const std::vector<std::string> &values, std::string &extract)
-{
-  int nlocal = atom->nlocal;
-  if (nlocal == nmax) grow(0);
-
-  h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp);
-  h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp);
-  extract = values[1];
-  if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
-    error->one(FLERR,"Invalid atom type in Atoms section of data file");
-
-  h_q[nlocal] = utils::numeric(FLERR,values[2],true,lmp);
-
-  h_x(nlocal,0) = coord[0];
-  h_x(nlocal,1) = coord[1];
-  h_x(nlocal,2) = coord[2];
-
-  h_image[nlocal] = imagetmp;
-
-  h_mask[nlocal] = 1;
-  h_v(nlocal,0) = 0.0;
-  h_v(nlocal,1) = 0.0;
-  h_v(nlocal,2) = 0.0;
-
-  atomKK->modified(Host,ALL_MASK);
-
-  atom->nlocal++;
-}
-/* ----------------------------------------------------------------------
-   unpack hybrid quantities from one line in Atoms section of data file
-   initialize other atom quantities for this sub-style
-------------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::data_atom_hybrid(int nlocal, const std::vector<std::string> &values,
-                                          int offset)
-{
-  h_q[nlocal] = utils::numeric(FLERR,values[offset],true,lmp);
-
-  return 1;
-}
-/* ----------------------------------------------------------------------
-   pack atom info for data file including 3 image flags
-------------------------------------------------------------------------- */
-
-void AtomVecChargeKokkos::pack_data(double **buf)
-{
-  int nlocal = atom->nlocal;
-  for (int i = 0; i < nlocal; i++) {
-    buf[i][0] = h_tag[i];
-    buf[i][1] = h_type[i];
-    buf[i][2] = h_q[i];
-    buf[i][3] = h_x(i,0);
-    buf[i][4] = h_x(i,1);
-    buf[i][5] = h_x(i,2);
-    buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX;
-    buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX;
-    buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX;
-  }
-}
-
-/* ----------------------------------------------------------------------
-   pack hybrid atom info for data file
-------------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::pack_data_hybrid(int i, double *buf)
-{
-  buf[0] = h_q[i];
-  return 1;
-}
-
-/* ----------------------------------------------------------------------
-   write atom info to data file including 3 image flags
-------------------------------------------------------------------------- */
-
-void AtomVecChargeKokkos::write_data(FILE *fp, int n, double **buf)
-{
-  for (int i = 0; i < n; i++)
-    fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n",
-            (int) buf[i][0],(int) buf[i][1],buf[i][2],buf[i][3],buf[i][4],buf[i][5],
-            (int) buf[i][6],(int) buf[i][7],(int) buf[i][8]);
-}
-
-/* ----------------------------------------------------------------------
-   write hybrid atom info to data file
-------------------------------------------------------------------------- */
-
-int AtomVecChargeKokkos::write_data_hybrid(FILE *fp, double *buf)
-{
-  fprintf(fp," %-1.16e",buf[0]);
-  return 1;
-}
-
-/* ----------------------------------------------------------------------
-   return # of bytes of allocated memory
-------------------------------------------------------------------------- */
-
-double AtomVecChargeKokkos::memory_usage()
-{
-  double bytes = 0;
-
-  if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
-  if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
-  if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
-  if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
-  if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
-  if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
-  if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3);
-
-  if (atom->memcheck("q")) bytes += memory->usage(q,nmax);
-
-  return bytes;
-}
-
-/* ---------------------------------------------------------------------- */
-
 void AtomVecChargeKokkos::sync(ExecutionSpace space, unsigned int mask)
 {
   if (space == Device) {
@@ -1120,6 +564,8 @@ void AtomVecChargeKokkos::modified(ExecutionSpace space, unsigned int mask)
   }
 }
 
+/* ---------------------------------------------------------------------- */
+
 void AtomVecChargeKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int mask)
 {
   if (space == Device) {
@@ -1158,4 +604,3 @@ void AtomVecChargeKokkos::sync_overlapping_device(ExecutionSpace space, unsigned
       perform_async_copy<DAT::tdual_float_1d>(atomKK->k_q,space);
   }
 }
-