Merge pull request #4481 from akohlmey/collected-small-fixes

Collected small fixes and changes

cmake/presets/kokkos-cuda.cmake

@@ -1,6 +1,5 @@
 # preset that enables KOKKOS and selects CUDA compilation with OpenMP
-# enabled as well. This preselects CC 5.0 as default GPU arch, since
+# enabled as well. The GPU architecture *must* match your hardware
-# that is compatible with all higher CC, but not the default CC 3.5
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)

doc/src/Commands_fix.rst

@@ -162,8 +162,8 @@ OPT.
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd/langevin <fix_pimd>`
    * :doc:`pimd/nvt <fix_pimd>`
-   * :doc:`pimd/langevin/bosonic <fix_pimd_bosonic>`
+   * :doc:`pimd/langevin/bosonic <fix_pimd>`
-   * :doc:`pimd/nvt/bosonic <fix_pimd_bosonic>`
+   * :doc:`pimd/nvt/bosonic <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
    * :doc:`poems <fix_poems>`

doc/src/Commands_removed.rst

@@ -170,6 +170,18 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
 and the :ref:`GPU package <PKG-GPU>` are maintained
 and allow running LAMMPS with GPU acceleration.
 
+Compute atom/molecule
+_____________________
+
+.. deprecated:: 11 Dec2015
+
+The atom/molecule command has been removed from LAMMPS since it was superseded
+by the more general and extensible "chunk infrastructure".  Here the system is
+partitioned in one of many possible ways - including using molecule IDs -
+through the :doc:`compute chunk/atom <compute_chunk_atom>` command and then
+summing is done using :doc:`compute reduce/chunk <compute_reduce_chunk>` Please
+refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
+
 Fix ave/spatial and fix ave/spatial/sphere
 ------------------------------------------
 

doc/src/Developer.rst

@@ -24,4 +24,5 @@ of time and requests from the LAMMPS user community.
    Classes
    Developer_platform
    Developer_utils
+   Developer_internal
    Developer_grid

doc/src/Developer_internal.rst

@@ -0,0 +1,113 @@
+
+Internal Styles
+---------------
+
+LAMMPS has a number of styles that are not meant to be used in an input
+file and thus are not documented in the :doc:`LAMMPS command
+documentation <Commands_all>`.  The differentiation between user
+commands and internal commands is through the case of the command name:
+user commands and styles are all lower case, internal styles are all
+upper case.  Internal styles are not called from the input file, but
+their classes are instantiated by other styles.  Often they are
+created by other styles to store internal data or to perform actions
+regularly at specific steps of the simulation.
+
+The paragraphs below document some of those styles that have general
+utility and may be used to avoid redundant implementation.
+
+DEPRECATED Styles
+^^^^^^^^^^^^^^^^^
+
+The styles called DEPRECATED (e.g. pair, bond, fix, compute, region, etc.)
+have the purpose to inform users that a specific style has been removed
+or renamed.  This is achieved by creating an alias for the deprecated
+style to the corresponding class.  For example, the fix style DEPRECATED
+is aliased to fix style ave/spatial and fix style ave/spatial/sphere with
+the following code:
+
+.. code-block:: c++
+
+   FixStyle(DEPRECATED,FixDeprecated);
+   FixStyle(ave/spatial,FixDeprecated);
+   FixStyle(ave/spatial/sphere,FixDeprecated);
+
+The individual class will then determine based on the style name
+what action to perform:
+
+- inform that the style has been removed and what style replaces it, if any, and then error out
+- inform that the style has been renamed and then either execute the replacement or error out
+- inform that the style is no longer required, and it is thus ignored and continue
+
+There is also a section in the user's guide for :doc:`removed commands
+and packages <Commands_removed>` with additional explanations.
+
+Internal fix styles
+^^^^^^^^^^^^^^^^^^^
+
+fix DUMMY
+"""""""""
+
+Most fix classes cannot be instantiated before the simulation box has
+been created since they access data that is only available then.
+However, in some cases it is required that a fix must be at or close to
+the top of the list of all fixes.  In those cases an instance of the
+DUMMY fix style may be created by calling ``Modify::add_fix()`` and then
+later replaced by calling ``Modify::replace_fix()``.
+
+fix STORE/ATOM
+""""""""""""""
+
+Fix STORE/ATOM can be used as persistent storage of per-atom data.
+
+**Syntax**
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID STORE/ATOM N1 N2 gflag rflag
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* STORE/ATOM = style name of this fix command
+* N1 = 1, N2 = 0 : data is per-atom vector = single value per atom
+* N1 > 1, N2 = 0 : data is per-atom array = N1 values per atom
+* N1 > 0, N2 > 0 : data is per-atom tensor = N1xN2 values per atom
+* gflag = 1 communicate per-atom values with ghost atoms, 0 do not update ghost atom data
+* rflag = 1 store per-atom value in restart file, 0 do not store data in restart
+
+Similar functionality is also available through using custom per-atom
+properties with :doc:`fix property/atom <fix_property_atom>`.  The
+choice between the two fixes should be based on whether the user should
+be able to access this per-atom data: if yes, then fix property/atom is
+preferred, otherwise fix STORE/ATOM.
+
+fix STORE/GLOBAL
+""""""""""""""""
+
+Fix STORE/GLOBAL can be used as persistent storage of global data with support for restarts
+
+**Syntax**
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID STORE/GLOBAL N1 N2
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* STORE/GLOBAL = style name of this fix command
+* N1 >=1 : number of global items to store
+* N2 = 1 : data is global vector of length N1
+* N2 > 1 : data is global N1xN2 array
+
+fix STORE/LOCAL
+"""""""""""""""
+
+Fix STORE/LOCAL can be used as persistent storage for local data
+
+**Syntax**
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID STORE/LOCAL Nreset Nvalues
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* STORE/LOCAL = style name of this fix command
+* Nreset = frequency at which local data is available
+* Nvalues = number of values per local item, that is the number of columns

doc/src/Howto_peri.rst

@@ -197,7 +197,7 @@ The LPS model has a force scalar state
 .. math::
 
    \underline{t} = \frac{3K\theta}{m}\underline{\omega}\,\underline{x} +
-   \alpha \underline{\omega}\,\underline{e}^{\rm d}, \qquad\qquad\textrm{(3)}
+   \alpha \underline{\omega}\,\underline{e}^\mathrm{d}, \qquad\qquad\textrm{(3)}
 
 with :math:`K` the bulk modulus and :math:`\alpha` related to the shear
 modulus :math:`G` as
@@ -242,14 +242,14 @@ scalar state are defined, respectively, as
 
 .. math::
 
-   \underline{e}^{\rm i}=\frac{\theta \underline{x}}{3}, \qquad
+   \underline{e}^\mathrm{i}=\frac{\theta \underline{x}}{3}, \qquad
-   \underline{e}^{\rm d} = \underline{e}- \underline{e}^{\rm i},
+   \underline{e}^\mathrm{d} = \underline{e}- \underline{e}^\mathrm{i},
 
 
 where the arguments of the state functions and the vectors on which they
 operate are omitted for simplicity. We note that the LPS model is linear
 in the dilatation :math:`\theta`, and in the deviatoric part of the
-extension :math:`\underline{e}^{\rm d}`.
+extension :math:`\underline{e}^\mathrm{d}`.
 
 .. note::
 

doc/src/Howto_triclinic.rst

@@ -249,23 +249,23 @@ as follows:
 
 .. math::
 
-  a   = & {\rm lx} \\
+  a   = & \mathrm{lx} \\
-  b^2 = &  {\rm ly}^2 +  {\rm xy}^2 \\
+  b^2 = &  \mathrm{ly}^2 + \mathrm{xy}^2 \\
-  c^2 = &  {\rm lz}^2 +  {\rm xz}^2 +  {\rm yz}^2 \\
+  c^2 = &  \mathrm{lz}^2 + \mathrm{xz}^2 + \mathrm{yz}^2 \\
-  \cos{\alpha} = & \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
+  \cos{\alpha} = & \frac{\mathrm{xy}*\mathrm{xz} + \mathrm{ly}*\mathrm{yz}}{b*c} \\
-  \cos{\beta}  = & \frac{\rm xz}{c} \\
+  \cos{\beta}  = & \frac{\mathrm{xz}}{c} \\
-  \cos{\gamma} = & \frac{\rm xy}{b} \\
+  \cos{\gamma} = & \frac{\mathrm{xy}}{b} \\
 
 The inverse relationship can be written as follows:
 
 .. math::
 
-  {\rm lx}   = & a \\
+  \mathrm{lx}   = & a \\
-  {\rm xy}   = & b \cos{\gamma}  \\
+  \mathrm{xy}   = & b \cos{\gamma}  \\
-  {\rm xz}   = & c \cos{\beta}\\
+  \mathrm{xz}   = & c \cos{\beta}\\
-  {\rm ly}^2 = & b^2 - {\rm xy}^2 \\
+  \mathrm{ly}^2 = & b^2 - \mathrm{xy}^2 \\
-  {\rm yz}   = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
+  \mathrm{yz}   = & \frac{b*c \cos{\alpha} - \mathrm{xy}*\mathrm{xz}}{\mathrm{ly}} \\
-  {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\
+  \mathrm{lz}^2 = & c^2 - \mathrm{xz}^2 - \mathrm{yz}^2 \\
 
 The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
 :math:`\gamma` can be printed out or accessed by computes using the

doc/src/Speed_compare.rst

@@ -44,11 +44,6 @@ section below for examples where this has been done.
   system the crossover (in single precision) is often about 50K-100K
   atoms per GPU.  When performing double precision calculations the
   crossover point can be significantly smaller.
-* Both KOKKOS and GPU package compute bonded interactions (bonds, angles,
-  etc) on the CPU.  If the GPU package is running with several MPI processes
-  assigned to one GPU, the cost of computing the bonded interactions is
-  spread across more CPUs and hence the GPU package can run faster in these
-  cases.
 * When using LAMMPS with multiple MPI ranks assigned to the same GPU, its
   performance depends to some extent on the available bandwidth between
   the CPUs and the GPU. This can differ significantly based on the
@@ -85,10 +80,10 @@ section below for examples where this has been done.
   code (with a performance penalty due to having data transfers between
   host and GPU).
 * The GPU package requires neighbor lists to be built on the CPU when using
-  exclusion lists, or a triclinic simulation box.
+  hybrid pair styles, exclusion lists, or a triclinic simulation box.
-* The GPU package can be compiled for CUDA or OpenCL and thus supports
+* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus supports
-  both, NVIDIA and AMD GPUs well. On NVIDIA hardware, using CUDA is typically
+  NVIDIA, AMD, and Intel GPUs well. On NVIDIA hardware, using CUDA is
-  resulting in equal or better performance over OpenCL.
+  typically resulting in equal or better performance over OpenCL.
 * OpenCL in the GPU package does theoretically also support Intel CPUs or
   Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL)
   is superior.

doc/src/bond_bpm_spring.rst

@@ -142,7 +142,7 @@ is accordingly replaced with a square root. This approximation assumes bonds
 are evenly distributed on a spherical surface and neglects constant prefactors
 which are irrelevant since only the ratio of volumes matters. This term may be
 used to adjust the Poisson's ratio. See the simulation in the
-examples/bpm/poissons_ratio directory for a demonstration of this effect.
+``examples/bpm/poissons_ratio`` directory for a demonstration of this effect.
 
 If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting
 (or adding) that bond's contribution.

doc/src/bond_bpm_spring_plastic.rst

@@ -110,7 +110,7 @@ the data file or restart files read by the :doc:`read_data
 * :math:`k`             (force/distance units)
 * :math:`\epsilon_c`    (unitless)
 * :math:`\gamma`        (force/velocity units)
-* :math:`\epsilon_p     (unit less)
+* :math:`\epsilon_p`    (unitless)
 
 See the :doc:`bpm/spring doc page <bond_bpm_spring>` for information on
 the *smooth*, *normalize*, *break*, *overlay/pair*, and *store/local*
@@ -133,16 +133,17 @@ Restart and other info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 This bond style writes the reference state and plastic history of each
-bond to :doc:`binary restart files <restart>`. Loading a restart
+bond to :doc:`binary restart files <restart>`. Loading a restart file
-file will properly restore bonds. However, the reference state is NOT
+will properly restore bonds. However, the reference state is NOT written
-written to data files. Therefore reading a data file will not
+to data files.  Therefore reading a data file will not restore bonds and
-restore bonds and will cause their reference states to be redefined.
+will cause their reference states to be redefined.
 
-The potential energy and the single() function of this bond style returns zero.
+The potential energy and the single() function of this bond style
-The single() function also calculates two extra bond quantities, the initial
+returns zero.  The single() function also calculates two extra bond
-distance :math:`r_0` and the current equilbrium length :math:`r_eq`. These extra
+quantities, the initial distance :math:`r_0` and the current equilibrium
-quantities can be accessed by the :doc:`compute bond/local <compute_bond_local>`
+length :math:`r_eq`. These extra quantities can be accessed by the
-command as *b1* and *b2*, respectively.
+:doc:`compute bond/local <compute_bond_local>` command as *b1* and *b2*,
+respectively.
 
 Restrictions
 """"""""""""

doc/src/bond_harmonic.rst

@@ -60,6 +60,8 @@ Related commands
 """"""""""""""""
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
+:doc:`bond style harmonic/shift <bond_harmonic_shift>`,
+:doc:`bond style harmonic/shift/cut <bond_harmonic_shift_cut>`
 
 Default
 """""""

doc/src/bond_harmonic_shift.rst

@@ -31,9 +31,15 @@ the potential
 
    E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
 
-where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance.
+where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the
-The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is
+critical distance.  The potential energy has the value
-:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
+:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`.  This
+bond style differs from :doc:`bond_style harmonic <bond_harmonic>`
+by the value of the potential energy.
+
+The equivalent spring constant value *K* for use with :doc:`bond_style
+harmonic <bond_harmonic>` can be computed using :math:`K =
+U_{\text{min}} / [(r_0-r_c)^2]`.
 
 The following coefficients must be defined for each bond type via the
 :doc:`bond_coeff <bond_coeff>` command as in the example above, or in
@@ -41,9 +47,7 @@ the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
 * :math:`U_{\text{min}}` (energy)
-
 * :math:`r_0` (distance)
-
 * :math:`r_c` (distance)
 
 ----------
@@ -63,7 +67,8 @@ Related commands
 """"""""""""""""
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
-:doc:`bond_harmonic <bond_harmonic>`
+:doc:`bond style harmonic <bond_harmonic>`,
+:doc:`bond style harmonic/shift/cut <bond_harmonic_shift_cut>`
 
 Default
 """""""

doc/src/bond_harmonic_shift_cut.rst

@@ -31,9 +31,14 @@ uses the potential
 
    E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
 
-where :math:`r_0` is the equilibrium bond distance, and rc the critical distance.
+where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the
-The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}`
+critical distance.  The bond potential is zero and thus its force also
-at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
+zero for distances :math:`r > r_c`.  The potential energy has the value
+:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`.
+
+The equivalent spring constant value *K* for use with :doc:`bond_style
+harmonic <bond_harmonic>` for :math:`r <= r_c`, can be computed using
+:math:`K = U_{\text{min}} / [(r_0-r_c)^2]`
 
 The following coefficients must be defined for each bond type via the
 :doc:`bond_coeff <bond_coeff>` command as in the example above, or in

doc/src/compute_cna_atom.rst

@@ -67,7 +67,7 @@ following relation should also be satisfied:
 
 .. math::
 
-  r_c + r_s > 2*{\rm cutoff}
+  r_c + r_s > 2*\mathrm{cutoff}
 
 where :math:`r_c` is the cutoff distance of the potential, :math:`r_s`
 is the skin

doc/src/compute_cnp_atom.rst

@@ -74,7 +74,7 @@ following relation should also be satisfied:
 
 .. math::
 
-  r_c + r_s > 2*{\rm cutoff}
+  r_c + r_s > 2*\mathrm{cutoff}
 
 where :math:`r_c` is the cutoff distance of the potential, :math:`r_s` is
 the skin

doc/src/compute_efield_wolf_atom.rst

@@ -50,9 +50,9 @@ the potential energy using the Wolf summation method, described in
 
 .. math::
    E_i = \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+   \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} +
    \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+   \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
 where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()*
 are error-function and complementary error-function terms.  This

doc/src/compute_hexorder_atom.rst

@@ -40,7 +40,7 @@ is a complex number (stored as two real numbers) defined as follows:
 
 .. math::
 
-   q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\bf r}_{ij})}
+   q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\textbf{r}}_{ij})}
 
 where the sum is over the *nnn* nearest neighbors
 of the central atom. The angle :math:`\theta`

doc/src/compute_orientorder_atom.rst

@@ -49,7 +49,7 @@ For each atom, :math:`Q_\ell` is a real number defined as follows:
 
 .. math::
 
-   \bar{Y}_{\ell m} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{\ell m}\bigl( \theta( {\bf r}_{ij} ), \phi( {\bf r}_{ij} ) \bigr) \\
+   \bar{Y}_{\ell m} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{\ell m}\bigl( \theta( \mathbf{r}_{ij} ), \phi( \mathbf{r}_{ij} ) \bigr) \\
    Q_\ell  = & \sqrt{\frac{4 \pi}{2 \ell  + 1} \sum_{m = -\ell }^{m = \ell } \bar{Y}_{\ell m} \bar{Y}^*_{\ell m}}
 
 The first equation defines the local order parameters as averages

doc/src/compute_sna_atom.rst

@@ -139,11 +139,11 @@ mapped on to a third polar angle :math:`\theta_0` defined by,
 
 .. math::
 
-  \theta_0 = {\sf rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
+  \theta_0 = \mathsf{rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
 
 In this way, all possible neighbor positions are mapped on to a subset
-of the 3-sphere.  Points south of the latitude :math:`\theta_0` =
+of the 3-sphere.  Points south of the latitude
-*rfac0* :math:`\pi` are excluded.
+:math:`\theta_0 = \mathsf{rfac0} \pi` are excluded.
 
 The natural basis for functions on the 3-sphere is formed by the
 representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi,
@@ -204,7 +204,7 @@ components summed separately for each LAMMPS atom type:
 
 .. math::
 
-   -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}  }}{\partial {\bf r}_i}
+   -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}  }}{\partial \mathbf{r}_i}
 
 The sum is over all atoms *i'* of atom type *I*\ .  For each atom *i*,
 this compute evaluates the above expression for each direction, each
@@ -216,7 +216,7 @@ derivatives:
 
 .. math::
 
-  -{\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i}
+  -\mathbf{r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial \mathbf{r}_i}
 
 Again, the sum is over all atoms *i'* of atom type *I*\ .  For each atom
 *i*, this compute evaluates the above expression for each of the six

doc/src/compute_stress_atom.rst

@@ -65,7 +65,7 @@ In case of compute *stress/atom*, the virial contribution is:
 
    W_{ab} & = \frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) + \frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b})  \\
   & + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\
-  & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
+  & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
 
 The first term is a pairwise energy contribution where :math:`n` loops
 over the :math:`N_p` neighbors of atom :math:`I`, :math:`\mathbf{r}_1`
@@ -97,7 +97,7 @@ In case of compute *centroid/stress/atom*, the virial contribution is:
 .. math::
 
    W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a}  F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\
-  & + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
+  & + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
 
 As with compute *stress/atom*, the first, second, third, fourth and
 fifth terms are pairwise, bond, angle, dihedral and improper

doc/src/fitpod_command.rst

@@ -263,10 +263,10 @@ then the globally defined weights from the ``fitting_weight_energy`` and
 POD Potential
 """""""""""""
 
-We consider a multi-element system of *N* atoms with :math:`N_{\rm e}`
+We consider a multi-element system of *N* atoms with :math:`N_\mathrm{e}`
 unique elements.  We denote by :math:`\boldsymbol r_n` and :math:`Z_n`
 position vector and type of an atom *n* in the system,
-respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e}
+respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_\mathrm{e}
 \}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots,
 \boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1,
 Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The total energy of the

doc/src/fix.rst

@@ -341,8 +341,8 @@ accelerated styles exist.
 * :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
 * :doc:`pimd/langevin <fix_pimd>` - Feynman path-integral molecular dynamics with stochastic thermostat
 * :doc:`pimd/nvt <fix_pimd>` - Feynman path-integral molecular dynamics with Nose-Hoover thermostat
-* :doc:`pimd/langevin/bosonic <fix_pimd_bosonic>` - Bosonic Feynman path-integral molecular dynamics for with stochastic thermostat
+* :doc:`pimd/langevin/bosonic <fix_pimd>` - Bosonic Feynman path-integral molecular dynamics for with stochastic thermostat
-* :doc:`pimd/nvt/bosonic <fix_pimd_bosonic>` - Bosonic Feynman path-integral molecular dynamics with Nose-Hoover thermostat
+* :doc:`pimd/nvt/bosonic <fix_pimd>` - Bosonic Feynman path-integral molecular dynamics with Nose-Hoover thermostat
 * :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
 * :doc:`plumed <fix_plumed>` - wrapper on PLUMED free energy library
 * :doc:`poems <fix_poems>` - constrain clusters of atoms to move as coupled rigid bodies

doc/src/fix_ave_chunk.rst

@@ -459,8 +459,8 @@ output.  This option can only be used with the *ave running* setting.
 
 The *format* keyword sets the numeric format of each value when it is
 printed to a file via the *file* keyword.  Note that all values are
-floating point quantities.  The default format is %g.  You can specify
+floating point quantities.  The default format is " %g".  You can specify
-a higher precision if desired (e.g., %20.16g).
+a higher precision if desired (e.g., " %20.16g").
 
 The *title1* and *title2* and *title3* keywords allow specification of
 the strings that will be printed as the first three lines of the output

doc/src/fix_ave_time.rst

@@ -304,8 +304,8 @@ output.  This option can only be used with the *ave running* setting.
 
 The *format* keyword sets the numeric format of each value when it is
 printed to a file via the *file* keyword.  Note that all values are
-floating point quantities.  The default format is %g.  You can specify
+floating point quantities.  The default format is " %g".  You can specify
-a higher precision if desired (e.g., %20.16g).
+a higher precision if desired (e.g., " %20.16g").
 
 The *title1* and *title2* and *title3* keywords allow specification of
 the strings that will be printed as the first 2 or 3 lines of the

doc/src/fix_gld.rst

@@ -60,9 +60,9 @@ With this fix active, the force on the *j*\ th atom is given as
 
 .. math::
 
-   {\bf F}_{j}(t) = & {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\
+   \mathbf{F}_{j}(t) = & \mathbf{F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) \mathbf{v}_j(s)~\text{d}s + \mathbf{F}^R_j(t) \\
    \Gamma_j(t-s) = & \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\
-   \langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s)
+   \langle\mathbf{F}^R_j(t),\mathbf{F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s)
 
 Here, the first term is representative of all conservative (pairwise,
 bonded, etc) forces external to this fix, the second is the temporally

doc/src/fix_halt.rst

@@ -25,13 +25,14 @@ Syntax
 * operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^"
 * avalue = numeric value to compare attribute to
 * zero or more keyword/value pairs may be appended
-* keyword = *error* or *message* or *path*
+* keyword = *error* or *message* or *path* or *universe*
 
   .. parsed-literal::
 
        *error* value = *hard* or *soft* or *continue*
        *message* value = *yes* or *no*
        *path* value = path to check for free space (may be in quotes)
+       *universe* value = *yes* or *no*
 
 
 Examples
@@ -40,8 +41,10 @@ Examples
 .. code-block:: LAMMPS
 
    fix 10 all halt 1 bondmax > 1.5
-   fix 10 all halt 10 v_myCheck != 0 error soft
+   fix 10 all halt 10 v_myCheck != 0 error soft message no
    fix 10 all halt 100 diskfree < 100000.0 path "dump storage/."
+   fix  2 all halt 100 v_curtime > ${maxtime} universe yes
+
 
 Description
 """""""""""
@@ -141,33 +144,52 @@ The optional *error* keyword determines how the current run is halted.
 If its value is *hard*, then LAMMPS will stop with an error message.
 
 If its value is *soft*, LAMMPS will exit the current run, but continue
-to execute subsequent commands in the input script.  However,
+to execute subsequent commands in the input script.  However, additional
-additional :doc:`run <run>` or :doc:`minimize <minimize>` commands will be
+:doc:`run <run>` or :doc:`minimize <minimize>` commands will be skipped.
-skipped.  For example, this allows a script to output the current
+For example, this allows a script to output the current state of the
-state of the system, e.g. via a :doc:`write_dump <write_dump>` or
+system, e.g. via a :doc:`write_dump <write_dump>` or :doc:`write_restart
-:doc:`write_restart <write_restart>` command.
+<write_restart>` command.  To re-enable regular runs after *fix halt*
+stopped a run, you need to issue a :doc:`timer timeout unlimited
+<timer>` command.
 
 If its value is *continue*, the behavior is the same as for *soft*,
 except subsequent :doc:`run <run>` or :doc:`minimize <minimize>` commands
 are executed.  This allows your script to remedy the condition that
-triggered the halt, if necessary.  Note that you may wish use the
+triggered the halt, if necessary.  This is the equivalent of stopping
-:doc:`unfix <unfix>` command on the fix halt ID, so that the same
+with *error soft* and followed by :doc:`timer timeout unlimited
-condition is not immediately triggered in a subsequent run.
+<timer>` command.  This can have undesired consequences, when a
+:doc:`run command <run>` uses the *every* keyword, so using *error soft*
+and resetting the timer manually may be the preferred option.
+
+You may wish use the :doc:`unfix <unfix>` command on the *fix halt* ID
+before starting a subsequent run, so that the same condition is not
+immediately triggered again.
 
 The optional *message* keyword determines whether a message is printed
 to the screen and logfile when the halt condition is triggered.  If
 *message* is set to yes, a one line message with the values that
-triggered the halt is printed.  If *message* is set to no, no message
+triggered the halt is printed.  If *message* is set to no, no message is
-is printed; the run simply exits.  The latter may be desirable for
+printed; the run simply exits.  The latter may be desirable for
 post-processing tools that extract thermodynamic information from log
 files.
 
+.. versionadded:: TBD
+
+The optional *universe* keyword determines whether the halt request
+should be synchronized across the partitions of a :doc:`multi-partition
+run <Run_options>`.  If *universe* is set to yes, fix halt will check if
+there is a specific message received from any of the other partitions
+requesting to stop the run on this partition as well.  Consequently, if
+fix halt determines to halt the simulation, the fix will send messages
+to all other partitions so they stop their runs, too.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.  No global or per-atom quantities are stored
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
-by this fix for access by various :doc:`output commands <Howto_output>`.
+relevant to this fix.  No global or per-atom quantities are stored by
+this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 
@@ -183,4 +205,4 @@ Related commands
 Default
 """""""
 
-The option defaults are error = soft, message = yes, and path = ".".
+The option defaults are error = soft, message = yes, path = ".", and universe = no.

doc/src/fix_lb_fluid.rst

@@ -130,7 +130,7 @@ calculated as:
 
 .. math::
 
-   {\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha}
+   \mathbf{F}_{j \alpha} = \gamma \left(\mathbf{v}_n - \mathbf{u}_f \right) \zeta_{j\alpha}
 
 where :math:`\mathbf{v}_n` is the velocity of the MD particle,
 :math:`\mathbf{u}_f` is the fluid velocity interpolated to the particle

doc/src/fix_nh.rst

@@ -208,19 +208,19 @@ The relaxation rate of the barostat is set by its inertia :math:`W`:
 
 .. math::
 
-   W = (N + 1) k_B T_{\rm target} P_{\rm damp}^2
+   W = (N + 1) k_B T_\mathrm{target} P_\mathrm{damp}^2
 
 where :math:`N` is the number of atoms, :math:`k_B` is the Boltzmann constant,
-and :math:`T_{\rm target}` is the target temperature of the barostat :ref:`(Martyna) <nh-Martyna>`.
+and :math:`T_\mathrm{target}` is the target temperature of the barostat :ref:`(Martyna) <nh-Martyna>`.
-If a thermostat is defined, :math:`T_{\rm target}` is the target temperature
+If a thermostat is defined, :math:`T_\mathrm{target}` is the target temperature
-of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}`
+of the thermostat. If a thermostat is not defined, :math:`T_\mathrm{target}`
 is set to the current temperature of the system when the barostat is initialized.
 If this temperature is too low the simulation will quit with an error.
-Note: in previous versions of LAMMPS, :math:`T_{\rm target}` would default to
+Note: in previous versions of LAMMPS, :math:`T_\mathrm{target}` would default to
 a value of 1.0 for *lj* units and 300.0 otherwise if the system had a temperature
 of exactly zero.
 
-If a thermostat is not specified by this fix, :math:`T_{\rm target}` can be
+If a thermostat is not specified by this fix, :math:`T_\mathrm{target}` can be
 manually specified using the *Ptemp* parameter. This may be useful if the
 barostat is initialized when the current temperature does not reflect the
 steady state temperature of the system. This keyword may also be useful in
@@ -512,8 +512,8 @@ according to the following factorization of the Liouville propagator
 .. math::
 
    \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E}
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\
    &\times \left[
@@ -526,8 +526,8 @@ according to the following factorization of the Liouville propagator
    &\times
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
    &+ \mathcal{O} \left(\Delta t^3 \right)
 
 This factorization differs somewhat from that of Tuckerman et al, in

doc/src/fix_npt_cauchy.rst

@@ -426,8 +426,8 @@ according to the following factorization of the Liouville propagator
 .. math::
 
    \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E}
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\
    &\times \left[
@@ -440,8 +440,8 @@ according to the following factorization of the Liouville propagator
    &\times
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
    &+ \mathcal{O} \left(\Delta t^3 \right)
 
 This factorization differs somewhat from that of Tuckerman et al, in

doc/src/fix_orient.rst

@@ -62,19 +62,19 @@ The potential energy added to atom I is given by these formulas
 
 .. math::
 
-   \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(1\right) \\
+   \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(1\right) \\
    \\
-  \xi_{\rm IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^{\rm J} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(2\right)\\
+  \xi_\mathrm{IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^\mathrm{J} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(2\right)\\
   \\
-  \xi_{\rm low}  = & {\rm cutlo} \, \xi_{\rm IJ}  \qquad\qquad\qquad\left(3\right)\\
+  \xi_\mathrm{low}  = & \mathrm{cutlo} \, \xi_\mathrm{IJ}  \qquad\qquad\qquad\left(3\right)\\
-  \xi_{\rm high}  = & {\rm cuthi} \, \xi_{\rm IJ} \qquad\qquad\qquad\left(4\right) \\
+  \xi_\mathrm{high}  = & \mathrm{cuthi} \, \xi_\mathrm{IJ} \qquad\qquad\qquad\left(4\right) \\
   \\
-  \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_{\rm low}}{\xi_{\rm high} - \xi_{\rm low}} \qquad\qquad\left(5\right)\\
+  \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_\mathrm{low}}{\xi_\mathrm{high} - \xi_\mathrm{low}} \qquad\qquad\left(5\right)\\
   \\
-  u_{i}  = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_{\rm low}\\
+  u_{i}  = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_\mathrm{low}\\
-         = & {\rm dE}\,\frac{1 - \cos(2 \omega_{i})}{2}
+         = & \mathrm{dE}\,\frac{1 - \cos(2 \omega_{i})}{2}
-   \qquad \mathrm{ for }\qquad \xi_{\rm low} < \xi_{i} < \xi_{\rm high}  \quad \left(6\right) \\
+   \qquad \mathrm{for }\qquad \xi_\mathrm{low} < \xi_{i} < \xi_\mathrm{high}  \quad \left(6\right) \\
-         = & {\rm dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_{\rm high} < \xi_{i}
+         = & \mathrm{dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_\mathrm{high} < \xi_{i}
 
 which are fully explained in :ref:`(Janssens) <Janssens>`.  For fcc crystals
 this order parameter Xi for atom I in equation (1) is a sum over the

doc/src/fix_pimd.rst

@@ -9,11 +9,11 @@ fix pimd/langevin command
 fix pimd/nvt command
 ====================
 
-:doc:`fix pimd/langevin/bosonic <fix_pimd_bosonic>` command
+fix pimd/langevin/bosonic command
-===========================================================
+=================================
 
-:doc:`fix pimd/nvt/bosonic <fix_pimd_bosonic>` command
+fix pimd/nvt/bosonic command
-======================================================
+============================
 
 Syntax
 """"""
@@ -23,7 +23,7 @@ Syntax
    fix ID group-ID style keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* style = *pimd/langevin* or *pimd/nvt* = style name of this fix command
+* style = *pimd/langevin* or *pimd/nvt* or *pimd/langevin/bosonic* or *pimd/nvt/bosonic* = style name of this fix command
 * zero or more keyword/value pairs may be appended
 * keywords for style *pimd/nvt*
 
@@ -89,19 +89,20 @@ partition function for the original system to a classical partition
 function for a ring-polymer system is exploited, to efficiently sample
 configurations from the canonical ensemble :ref:`(Feynman) <Feynman>`.
 
-.. versionadded:: 11Mar2025
+.. versionadded:: TBD
 
    Fix *pimd/langevin/bosonic* and *pimd/nvt/bosonic* were added.
 
 Fix *pimd/nvt* and fix *pimd/langevin* simulate *distinguishable* quantum particles.
-Simulations of bosons, including exchange effects, are supported with the :doc:`fix pimd/langevin/bosonic <fix_pimd_bosonic>` and :doc:`fix pimd/nvt/bosonic <fix_pimd_bosonic>` commands.
+Simulations of bosons, including exchange effects, are supported with the
+fix *pimd/langevin/bosonic* and the *pimd/nvt/bosonic* commands.
 
 For distinguishable particles, the isomorphic classical partition function and its components are given
 by the following equations:
 
 .. math::
 
-   Z = & \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\
+   Z = & \int d\mathbf{q} d\mathbf{p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\
    H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2M_i}\bigg) + V_{eff} \\
    V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
 
@@ -173,15 +174,17 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
 
    Mode *pimd* added to fix pimd/langevin.
 
-Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default value is *nmpimd*.
+Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default
-If *method* is *nmpimd*, the normal mode representation is used to integrate the equations of motion.
+value is *nmpimd*.  If *method* is *nmpimd*, the normal mode representation is
-The exact solution of harmonic oscillator is used to propagate the free ring polymer part of the Hamiltonian.
+used to integrate the equations of motion.  The exact solution of harmonic
-If *method* is *pimd*, the Cartesian representation is used to integrate the equations of motion.
+oscillator is used to propagate the free ring polymer part of the Hamiltonian.
-The harmonic force is added to the total force of the system, and the numerical integrator is used to propagate the Hamiltonian.
+If *method* is *pimd*, the Cartesian representation is used to integrate the
+equations of motion.  The harmonic force is added to the total force of the
+system, and the numerical integrator is used to propagate the Hamiltonian.
 
-The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*.
+The keyword *integrator* specifies the Trotter splitting method used by *fix
-See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB splitting schemes. Typically
+pimd/langevin*.  See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB
-either of the two should work fine.
+splitting schemes. Typically either of the two should work fine.
 
 The keyword *fmass* sets a further scaling factor for the fictitious
 masses of beads, which can be used for the Partial Adiabatic CMD
@@ -231,8 +234,8 @@ a positive floating-point number.
    For pimd simulations, a temperature values should be specified even for nve ensemble. Temperature will make a difference
    for nve pimd, since the spring elastic frequency between the beads will be affected by the temperature.
 
-The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. *style* can only
+The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*.
-be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
+*style* can only be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
 
 .. note::
 
@@ -418,7 +421,12 @@ LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
 Fix *pimd/nvt* cannot be used with :doc:`lj units <units>`.
-Fix *pimd/langevin* can be used with :doc:`lj units <units>`. See the above part for how to use it.
+Fix *pimd/langevin* can be used with :doc:`lj units <units>`.
+See the documentation above for how to use it.
+
+Only some combinations of fix styles and their options support
+partitions with multiple processors.  LAMMPS will stop with an
+error if multi-processor partitions are not supported.
 
 A PIMD simulation can be initialized with a single data file read via
 the :doc:`read_data <read_data>` command.  However, this means all
@@ -435,7 +443,7 @@ variable, e.g.
 Related commands
 """"""""""""""""
 
-:doc:`pimd/nvt/bosonic <fix_pimd_bosonic>`, :doc:`pimd/langevin/bosonic <fix_pimd_bosonic>`
+:doc:`fix ipi <fix_ipi>`
 
 Default
 """""""

doc/src/fix_pimd_bosonic.rst

@@ -1,237 +0,0 @@
-.. index:: fix pimd/langevin/bosonic
-.. index:: fix pimd/nvt/bosonic
-
-fix pimd/langevin/bosonic command
-=================================
-
-fix pimd/nvt/bosonic command
-============================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   fix ID group-ID style keyword value ...
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* style = *pimd/langevin/bosonic* or *pimd/nvt/bosonic* = style name of this fix command
-* zero or more keyword/value pairs may be appended
-* keywords for style *pimd/nvt/bosonic*
-
-  .. parsed-literal::
-
-     *keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
-     *method* value = *pimd* or *nmpimd*
-     *fmass* value = scaling factor on mass
-     *sp* value = scaling factor on Planck constant
-     *temp* value = temperature (temperature units)
-     *nhc* value = Nc = number of chains in Nose-Hoover thermostat
-
-* keywords for style *pimd/langevin/bosonic*
-
-  .. parsed-literal::
-
-     *keywords* = *integrator* or *ensemble* or *fmass* or *temp* or *thermostat* or *tau* or *fixcom* or *lj* or *esych*
-     *integrator* value = *obabo* or *baoab*
-     *ensemble* value = *nvt* or *nve*
-     *fmass* value = scaling factor on mass
-     *temp* value = temperature (temperature unit)
-          temperature = target temperature of the thermostat
-     *thermostat* values = style seed
-          style value = *PILE_L*
-          seed = random number generator seed
-     *tau* value = thermostat damping parameter (time unit)
-     *fixcom* value = *yes* or *no*
-     *lj* values = epsilon sigma mass planck mvv2e
-          epsilon = energy scale for reduced units (energy units)
-          sigma = length scale for reduced units (length units)
-          mass = mass scale for reduced units (mass units)
-          planck = Planck's constant for other unit style
-          mvv2e = mass * velocity^2 to energy conversion factor for other unit style
-     *esynch* value = *yes* or *no*
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 1 all pimd/nvt/bosonic method pimd fmass 1.0 sp 1.0 temp 2.0 nhc 4
-   fix 1 all pimd/langevin/bosonic integrator obabo temp 113.15 thermostat PILE_L 1234 tau 1.0
-
-Example input files are provided in the examples/PACKAGES/pimd_bosonic directory.
-
-Description
-"""""""""""
-
-These fix commands are based on the fixes :doc:`pimd/nvt and
-pimd/langevin <fix_pimd>` for performing quantum molecular dynamics
-simulations based on the Feynman path-integral formalism. The key
-difference is that fix *pimd/nvt* and fix *pimd/langevin* simulate
-*distinguishable* particles, while fix *pimd/nvt/bosonic* and fix
-*pimd/langevin/bosonic* perform simulations of bosons, including exchange
-effects. The *bosonic* commands share syntax with the equivalent commands for distinguishable particles.
-The user is referred to the documentation of :doc:`these commands <fix_pimd>`
-for a detailed syntax description and additional, general capabilities
-of the commands. The major differences from fix *pimd/nvt* and fix *pimd/langevin* in terms of
-capabilities are:
-
-* Fix *pimd/nvt/bosonic* only supports the "pimd" and "nmpimd" methods. Fix
-  *pimd/langevin/bosonic* only supports the "pimd" method, which is the default
-  in this fix. These restrictions are related to the use of normal
-  modes, which change in bosons. For similar reasons, *fmmode* of
-  *pimd/langevin* should not be used, and would raise an error if set to
-  a value other than *physical*.
-* Fix *pimd/langevin/bosonic* currently does not support *ensemble* other than
-  *nve*, *nvt*. The barostat related keywords *iso*, *aniso*,
-  *barostat*, *taup* are not supported.
-* Fix *pimd/langevin/bosonic* also has a keyword not available in fix
-  *pimd/langevin*: *esynch*, with default *yes*. If set to *no*, some
-  time consuming synchronization of spring energies and the primitive
-  kinetic energy estimator between processors is avoided.
-
-The isomorphism between the partition function of :math:`N` bosonic
-quantum particles and that of a system of classical ring polymers at
-inverse temperature :math:`\beta` is given by :ref:`(Tuckerman)
-<book-Tuckerman>`:
-
-.. math::
-
-   Z \propto \int d{\bf q} \cdot \frac{1}{N!} \sum_\sigma \textrm{exp} [ -\beta \left( E^\sigma + V \right) ].
-
-Here, :math:`V` is the potential between different particles at the same
-imaginary time slice, which is the same for bosons and distinguishable
-particles. The sum is over all permutations :math:`\sigma`. Recall that
-a permutation matches each element :math:`l` in :math:`1, ..., N` to an
-element :math:`\sigma(l)` in :math:`1, ..., N` without repetitions. The
-energies :math:`E^\sigma` correspond to the linking of ring polymers of
-different particles according to the permutations:
-
-.. math::
-
-   E^\sigma = \frac{mP}{2\beta^2 \hbar^2} \sum_{\ell=1}^N \sum_{j=1}^P \left(\mathbf{q}_\ell^j - \mathbf{q}_\ell^{j+1}\right)^2,
-
-where :math:`P` is the number of beads and :math:`\mathbf{q}_\ell^{P+1}=\mathbf{q}_{\sigma(\ell)}^1.`
-
-Hirshberg et. al. showed that the ring polymer potential
-:math:`-\frac{1}{\beta}\textrm{ln}\left[ \frac{1}{N!} \sum_\sigma e ^ {
--\beta E^\sigma } \right]`, which scales exponentially with :math:`N`,
-can be replaced by a potential :math:`V^{[1,N]}` defined through a
-recurrence relation :ref:`(Hirshberg1) <Hirshberg>`:
-
-.. math::
-
-   e ^ { -\beta  V^{[1,N]} } = \frac{1}{N} \sum_{k=1}^N e ^ { -\beta \left(  V^{[1,N-k]} + E^{[N-K+1,N]} \right)}.
-
-Here, :math:`E^{[N-K+1,N]}` is the spring energy of the ring polymer
-obtained by connecting the beads of particles :math:`N - k + 1, N - k +
-2, ..., N` in a cycle.  This potential does not include all :math:`N!`
-permutations, but samples the same bosonic partition function. The
-implemented algorithm in LAMMPS for calculating the potential is the one
-developed by Feldman and Hirshberg, which scales like :math:`N^2+PN`
-:ref:`(Feldman) <Feldman>`.  The forces are calculated as weighted
-averages over the representative permutations, through an algorithm that
-scales the same as the one for the potential calculation, :math:`N^2+PN`
-:ref:`(Feldman) <Feldman>`.  The minimum-image convention is employed on
-the springs to account for periodic boundary conditions; an elaborate
-discussion of the validity of the approximation is available in
-:ref:`(Higer) <HigerFeldman>`.
-
-Restart, fix_modify, output, run start/stop, minimize info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-The use of :doc:`binary restart files <restart>` and :doc:`fix_modify
-<fix_modify>` is the same as in :doc:`fix pimd <fix_pimd>`.
-
-Fix *pimd/nvt/bosonic* computes a global 4-vector, which can be accessed by
-various :doc:`output commands <Howto_output>`.  The quantities in
-the global vector are:
-
-   #. the total spring energy of the quasi-beads,
-   #. the current temperature of the classical system of ring polymers,
-   #. the current value of the scalar virial estimator for the kinetic
-      energy of the quantum system :ref:`(Herman) <HermanBB>` (see the justification in the supporting information of :ref:`(Hirshberg2) <HirshbergInvernizzi>`),
-   #. the current value of the scalar primitive estimator for the kinetic
-      energy of the quantum system :ref:`(Hirshberg1) <Hirshberg>`.
-
-The vector values calculated by fix *pimd/nvt/bosonic* are "extensive", except
-for the temperature, which is "intensive".
-
-Fix *pimd/langevin/bosonic* computes a global 6-vector, which can be accessed
-by various :doc:`output commands <Howto_output>`. The quantities in the
-global vector are:
-
-   #. kinetic energy of the beads,
-   #. spring elastic energy of the beads,
-   #. potential energy of the bead,
-   #. total energy of all beads (conserved if *ensemble* is *nve*) if *esynch* is *yes*
-   #. primitive kinetic energy estimator :ref:`(Hirshberg1) <Hirshberg>`
-   #. virial energy estimator :ref:`(Herman) <HermanBB>` (see the justification in the supporting information of :ref:`(Hirshberg2) <HirshbergInvernizzi>`).
-
-The first three are different for different log files, and the others
-are the same for different log files, except for the primitive kinetic
-energy estimator when setting *esynch* to *no*. Then, the primitive
-kinetic energy estimator is obtained by summing over all log files.
-Also note that when *esynch* is set to *no*, the fourth output gives the
-total energy of all beads excluding the spring elastic energy; the total
-classical energy can then be obtained by adding the sum of second output
-over all log files.  All vector values calculated by fix
-*pimd/langevin/bosonic* are "extensive".
-
-For both *pimd/nvt/bosonic* and *pimd/langevin/bosonic*, the contribution of the
-exterior spring to the primitive estimator is printed to the first log
-file.  The contribution of the :math:`P-1` interior springs is printed
-to the other :math:`P-1` log files.  The contribution of the constant
-:math:`\frac{PdN}{2 \beta}` (with :math:`d` being the dimensionality) is
-equally divided over log files.
-
-Restrictions
-""""""""""""
-
-These fixes are part of the REPLICA package.  They are only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package
-<Build_package>` page for more info.
-
-The restrictions of :doc:`fix pimd <fix_pimd>` apply.
-
-Related commands
-""""""""""""""""
-
-:doc:`pimd/nvt <fix_pimd>`, :doc:`pimd/langevin <fix_pimd>`
-
-Default
-"""""""
-
-The keyword defaults for fix *pimd/nvt/bosonic* are method = pimd, fmass = 1.0,
-sp = 1.0, temp = 300.0, and nhc = 2.
-
-The keyword defaults for fix *pimd/langevin/bosonic* are integrator = obabo,
-method = pimd, ensemble = nvt, fmass = 1.0, temp = 298.15, thermostat =
-PILE_L, tau = 1.0, fixcom = yes, esynch = yes, and lj = 1 for all its
-arguments.
-
-----------
-
-.. _book-Tuckerman:
-
-**(Tuckerman)** M. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation (Oxford University Press, 2010)
-
-.. _Hirshberg:
-
-**(Hirshberg1)** B. Hirshberg, V. Rizzi, and M. Parrinello, "Path integral molecular dynamics for bosons," Proc. Natl. Acad. Sci. U. S. A. 116, 21445 (2019)
-
-.. _HirshbergInvernizzi:
-
-**(Hirshberg2)** B. Hirshberg, M. Invernizzi, and M. Parrinello, "Path integral molecular dynamics for fermions: Alleviating the sign problem with the Bogoliubov inequality," J Chem Phys, 152, 171102 (2020)
-
-.. _Feldman:
-
-**(Feldman)** Y. M. Y. Feldman and B. Hirshberg, "Quadratic scaling bosonic path integral molecular dynamics," J. Chem. Phys. 159, 154107 (2023)
-
-.. _HigerFeldman:
-
-**(Higer)** J. Higer, Y. M. Y. Feldman, and B. Hirshberg, "Periodic Boundary Conditions for Bosonic Path Integral Molecular Dynamics," arXiv:2501.17618 (2025)
-
-.. _HermanBB:
-
-**(Herman)** M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).

doc/src/fix_reaxff_species.rst

@@ -207,6 +207,9 @@ No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 This fix is not invoked during :doc:`energy minimization <minimize>`.
 
+This fix supports dynamic groups only if the *Nrepeat* setting is 1,
+i.e. there is no averaging.
+
 ----------
 
 .. include:: accel_styles.rst

doc/src/min_modify.rst

@@ -98,14 +98,14 @@ all atoms
 
 .. math::
 
-   || \vec{F} ||_{max} = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
+   || \vec{F} ||_{max} = \mathrm{max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
 
 The *inf* norm takes the maximum component across the forces of
 all atoms in the system:
 
 .. math::
 
-   || \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right)
+   || \vec{F} ||_{inf} = \mathrm{max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right)
 
 For the min styles *spin*, *spin/cg* and *spin/lbfgs*, the force
 norm is replaced by the spin-torque norm.

doc/src/min_spin.rst

@@ -50,9 +50,9 @@ system:
 
 .. math::
 
-   {\Delta t}_{\rm max} = \frac{2\pi}{\kappa \left|\vec{\omega}_{\rm max} \right|}
+   {\Delta t}_\mathrm{max} = \frac{2\pi}{\kappa \left|\vec{\omega}_\mathrm{max} \right|}
 
-with :math:`\left|\vec{\omega}_{\rm max}\right|` the norm of the largest precession
+with :math:`\left|\vec{\omega}_\mathrm{max}\right|` the norm of the largest precession
 frequency in the system (across all processes, and across all replicas if a
 spin/neb calculation is performed).
 

doc/src/minimize.rst

@@ -108,12 +108,12 @@ potential energy of the system as a function of the N atom
 coordinates:
 
 .. math::
- E(r_1,r_2, \ldots ,r_N)  = & \sum_{i,j} E_{\it pair}(r_i,r_j) +
+ E(r_1,r_2, \ldots ,r_N)  = & \sum_{i,j} E_{pair}(r_i,r_j) +
-                              \sum_{ij} E_{\it bond}(r_i,r_j) +
+                              \sum_{ij} E_{bond}(r_i,r_j) +
-                              \sum_{ijk} E_{\it angle}(r_i,r_j,r_k) + \\
+                              \sum_{ijk} E_{angle}(r_i,r_j,r_k) + \\
-                            & \sum_{ijkl} E_{\it dihedral}(r_i,r_j,r_k,r_l) +
+                            & \sum_{ijkl} E_{dihedral}(r_i,r_j,r_k,r_l) +
-                              \sum_{ijkl} E_{\it improper}(r_i,r_j,r_k,r_l) +
+                              \sum_{ijkl} E_{improper}(r_i,r_j,r_k,r_l) +
-                              \sum_i E_{\it fix}(r_i)
+                              \sum_i E_{fix}(r_i)
 
 where the first term is the sum of all non-bonded :doc:`pairwise
 interactions <pair_style>` including :doc:`long-range Coulombic

doc/src/neb_spin.rst

@@ -148,7 +148,7 @@ spin i, :math:`\omega_i^{\nu}` is a rotation angle defined as:
 
 .. math::
 
-   \omega_i^{\nu} = (\nu - 1) \Delta \omega_i {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
+   \omega_i^{\nu} = (\nu - 1) \Delta \omega_i \mathrm{~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
 
 with :math:`\nu` the image number, Q the total number of images, and
 :math:`\omega_i` the total rotation between the initial and final spins.

doc/src/pair_aip_water_2dm.rst

@@ -53,14 +53,14 @@ materials as described in :ref:`(Feng1) <Feng1>` and :ref:`(Feng2) <Feng2>`.
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
-   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\
-   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_coul.rst

@@ -241,9 +241,9 @@ summation method, described in :ref:`Wolf <Wolf1>`, given by:
 .. math::
 
    E_i = \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+   \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} +
    \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+   \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
 where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()*
 are error-function and complementary error-function terms.  This

doc/src/pair_coul_shield.rst

@@ -40,8 +40,8 @@ the pair style :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
 .. math::
 
    E      = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
+   V_{ij} = & \mathrm{Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
-   {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                           70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                           84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                           35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_dpd_ext.rst

@@ -62,8 +62,8 @@ a sum of 3 terms
 
    \mathbf{f}  = & f^C + f^D + f^R \qquad \qquad r < r_c \\
    f^C      = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\
-   f^D      = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij}  - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\
+   f^D      = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij}  - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^\mathrm{T} ) \mathbf{v}_{ij} \\
-   f^R      = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij}  + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\
+   f^R      = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij}  + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^\mathrm{T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\
    w(r)     = & 1 - r/r_c \\
 
 where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D`

doc/src/pair_hbond_dreiding.rst

@@ -68,21 +68,21 @@ force field, given by:
 
 .. math::
 
-   E  = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_{\rm in} \\
+   E  = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_\mathrm{in} \\
-      = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
+      = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_\mathrm{in} < r < r_\mathrm{out} \\
-      = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_{\rm out} \\
+      = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_\mathrm{out} \\
    LJ(r)  = & AR^{-12}-BR^{-10}cos^n\theta=
          \epsilon\left\lbrace 5\left[ \frac{\sigma}{r}\right]^{12}-
          6\left[ \frac{\sigma}{r}\right]^{10}  \right\rbrace cos^n\theta\\
    Morse(r)  = & D_0\left\lbrace \chi^2 - 2\chi\right\rbrace cos^n\theta=
          D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)}
          \right\rbrace cos^n\theta \\
-   S(r)  = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
+   S(r)  = & \frac{ \left[r_\mathrm{out}^2 - r^2\right]^2
-   \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
+   \left[r_\mathrm{out}^2 + 2r^2 - 3{r_\mathrm{in}^2}\right]}
-   { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
+   { \left[r_\mathrm{out}^2 - {r_\mathrm{in}}^2\right]^3 }
 
-where :math:`r_{\rm in}` is the inner spline distance cutoff,
+where :math:`r_\mathrm{in}` is the inner spline distance cutoff,
-:math:`r_{\rm out}` is the outer distance cutoff, :math:`\theta_c` is
+:math:`r_\mathrm{out}` is the outer distance cutoff, :math:`\theta_c` is
 the angle cutoff, and :math:`n` is the power of the cosine of the angle
 :math:`\theta`.
 
@@ -189,8 +189,8 @@ follows:
 * :math:`\epsilon` (energy units)
 * :math:`\sigma` (distance units)
 * *n* = exponent in formula above
-* distance cutoff :math:`r_{\rm in}` (distance units)
+* distance cutoff :math:`r_\mathrm{in}` (distance units)
-* distance cutoff :math:`r_{\rm out}` (distance units)
+* distance cutoff :math:`r_\mathrm{out}` (distance units)
 * angle cutoff (degrees)
 
 For the *hbond/dreiding/morse* style the list of coefficients is as
@@ -202,7 +202,7 @@ follows:
 * :math:`\alpha` (1/distance units)
 * :math:`r_0` (distance units)
 * *n* = exponent in formula above
-* distance cutoff :math:`r_{\rm in}` (distance units)
+* distance cutoff :math:`r_\mathrm{in}` (distance units)
 * distance cutoff :math:`r_{out}` (distance units)
 * angle cutoff (degrees)
 

doc/src/pair_ilp_graphene_hbn.rst

@@ -44,14 +44,14 @@ in :ref:`(Kolmogorov) <Kolmogorov2>`.
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
-   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\
-   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_ilp_tmd.rst

@@ -41,14 +41,14 @@ as described in :ref:`(Ouyang7) <Ouyang7>` and :ref:`(Jiang) <Jiang>`.
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
-   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\
-   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
@@ -67,7 +67,7 @@ calculating the normals.
    normal vectors used for graphene and h-BN is no longer valid for TMDs.
    In :ref:`(Ouyang7) <Ouyang7>`, a new definition is proposed, where for
    each atom `i`, its six nearest neighboring atoms belonging to the same
-   sub-layer are chosen to define the normal vector `{\bf n}_i`.
+   sub-layer are chosen to define the normal vector `\mathbf{n}_i`.
 
 The parameter file (e.g. TMD.ILP), is intended for use with *metal*
 :doc:`units <units>`, with energies in meV. Two additional parameters,

doc/src/pair_kolmogorov_crespi_full.rst

@@ -37,8 +37,8 @@ No simplification is made,
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
    V_{ij}  = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) \right ] - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \\
-  \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\
+  \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij}\cdot \mathbf{n}_{i})^2 \\
-  \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij}\cdot  {\bf n}_{j})^2 \\
+  \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij}\cdot  \mathbf{n}_{j})^2 \\
   f(\rho) & =  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n}
 
 It is important to have a sufficiently large cutoff to ensure smooth

doc/src/pair_lj_cut_coul.rst

@@ -194,9 +194,9 @@ summation method, described in :ref:`Wolf <Wolf3>`, given by:
 .. math::
 
    E_i = \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+   \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} +
    \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+   \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
 where :math:`\alpha` is the damping parameter, and erfc() is the
 complementary error-function terms.  This potential is essentially a

doc/src/pair_mesodpd.rst

@@ -200,7 +200,7 @@ force :math:`F_{ij}^C` are expressed as
   \mathbf{F}_{ij}^{D} & = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij}  \\
   \mathbf{F}_{ij}^{R} & = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij} \\
   \omega_{C}(r) & = 1 - r/r_c \\
-  \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^{\rm power_f} \\
+  \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^\mathrm{power_f} \\
   \sigma^2 = 2\gamma k_B T
 
 The concentration flux between two tDPD particles includes the Fickian
@@ -211,7 +211,7 @@ by
 
    Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\
    Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\
-   w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power_{cc}} \\
+   w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^\mathrm{power_{cc}} \\
    \epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho
 
 where the parameters kappa and epsilon determine the strength of the

doc/src/pair_mgpt.rst

@@ -33,7 +33,7 @@ elemental bulk material in the form
 
 .. math::
 
-   E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega )
+   E_\mathrm{tot}(\mathbf{R}_1 \ldots \mathbf{R}_N) = NE_\mathrm{vol}(\Omega )
    + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega )
    + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega )
    + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega )

doc/src/pair_saip_metal.rst

@@ -41,14 +41,14 @@ potential (ILP) potential for hetero-junctions formed with hexagonal
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
-   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\
-   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
@@ -63,8 +63,8 @@ calculating the normals.
 .. note::
 
    To account for the isotropic nature of the isolated gold atom
-   electron cloud, their corresponding normal vectors (`{\bf n}_i`) are
+   electron cloud, their corresponding normal vectors (`\mathbf{n}_i`) are
-   assumed to lie along the interatomic vector `{\bf r}_ij`. Notably, this
+   assumed to lie along the interatomic vector `\mathbf{r}_ij`. Notably, this
    assumption is suitable for many bulk material surfaces, for
    example, for systems possessing s-type valence orbitals or
    metallic surfaces, whose valence electrons are mostly

doc/src/pair_spin_dipole.rst

@@ -43,7 +43,7 @@ vector omega and mechanical force between particles I and J.
 
 .. math::
 
-   \mathcal{H}_{\rm long} & =
+   \mathcal{H}_\mathrm{long} & =
    -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi}
    \sum_{i,j,i\neq j}^{N}
     \frac{g_i g_j}{r_{ij}^3}

doc/src/pair_spin_dmi.rst

@@ -52,7 +52,7 @@ particle i:
 .. math::
 
     \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right)
-    ~~{\rm and}~~
+    ~~\mathrm{and}~~
     \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right)
 
 More details about the derivation of these torques/forces are reported in

doc/src/pair_spin_exchange.rst

@@ -94,7 +94,7 @@ submitted to a force :math:`\vec{F}_{i}` for spin-lattice calculations (see
 
    \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
    \left(r_{ij} \right)\,\vec{s}_{j}
-   ~~{\rm and}~~
+   ~~\mathrm{and}~~
    \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
    \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
 

doc/src/region2vmd.rst

@@ -35,7 +35,7 @@ Description
 
 .. versionadded:: TBD
 
-Write a `VMD <https:://ks.uiuc.edu/Research/vmd/>`_ Tcl script file with
+Write a `VMD <https://ks.uiuc.edu/Research/vmd/>`_ Tcl script file with
 commands that aim to create a visualization of :doc:`regions <region>`.
 There may be multiple region visualizations stored in a single file.
 

doc/src/variable.rst

@@ -51,12 +51,12 @@ Syntax
          thermo keywords = vol, ke, press, etc from :doc:`thermo_style <thermo_style>`
          math operators = (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y,
                           x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x
-         math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
+         math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), sign(x),
                           sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
                           random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z),
                           ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
                           logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
-                          vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x)
+                          vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
          group functions = count(group), mass(group), charge(group),
                            xcm(group,dim), vcm(group,dim), fcm(group,dim),
                            bound(group,dir), gyration(group), ke(group),
@@ -541,7 +541,7 @@ variables.
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Math operators         | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x                                                                                                                                                                                                                                       |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| Math functions         | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x)  |
+| Math functions         | sqrt(x), exp(x), ln(x), log(x), abs(x), sign(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)  |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Group functions        | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim)                                                                                                                                                                             |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -692,6 +692,11 @@ sqrt() of the product of one atom's y and z coordinates.
 Most of the math functions perform obvious operations.  The ln() is
 the natural log; log() is the base 10 log.
 
+.. versionadded:: 4Feb2025
+
+The sign(x) function returns 1.0 if the value is greater than or equal
+to 0.0, and -1.0 otherwise.
+
 The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z =
 seed.  It generates a uniform random number between lo and hi.  The
 normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and
@@ -860,9 +865,6 @@ run, according to one of these formulas, where omega = 2 PI / period:
 
 where dt = the timestep size.
 
-The sign(x) function returns 1.0 if the value is greater than or equal
-to 0.0, and -1.0 otherwise.
-
 The run begins on startstep.  Startstep can span multiple runs, using
 the *start* keyword of the :doc:`run <run>` command.  See the :doc:`run
 <run>` command for details of how to do this.  Note that the

doc/utils/requirements.txt

@@ -1,4 +1,4 @@
-Sphinx >= 5.3.0, <8.2.0
+Sphinx >= 5.3.0, <8.3.0
 sphinxcontrib-spelling
 sphinxcontrib-jquery
 sphinx-design

doc/utils/sphinx-config/conf.py.in

@@ -208,13 +208,11 @@ html_favicon = '_static/lammps.ico'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ['_static',]
 
 # These paths are either relative to html_static_path
 # or fully qualified paths (eg. https://...)
-html_css_files = [
+html_css_files = ['css/lammps.css',]
-    'css/lammps.css',
-]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -290,7 +288,7 @@ rst_prolog = r"""
 
 .. only:: html
 
-   :math:`\renewcommand{\AA}{\text{Å}}`
+   :math:`\renewcommand{\AA}{\textup{\r{A}}`
 
 .. role:: lammps(code)
     :language: LAMMPS

doc/utils/sphinx-config/false_positives.txt

@@ -1331,6 +1331,7 @@ geturl
 gewald
 Gezelter
 gfile
+gflag
 Gflop
 gfortran
 ghostneigh
@@ -2964,6 +2965,7 @@ pKa
 pKb
 pKs
 planeforce
+plastically
 Plathe
 Plimpton
 plog
@@ -3266,6 +3268,7 @@ rewrap
 rezwanur
 rfac
 rfile
+rflag
 rg
 Rg
 Rhaphson

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++

@@ -0,0 +1,2 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
+Running on 4 partitions of processors

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 0
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -103,8 +104,8 @@ Initializing PI Langevin equation thermostat...
       3     9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
   PILE_L thermostat successfully initialized!
 
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              1.3661449e-08  0.0009918329 
@@ -208,20 +209,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
         98   9.2042324e-06  1.780703e-05   0.00083221292
         99   9.5058078e-06  1.8141862e-05  0.00082913227
        100   9.8087647e-06  1.8457846e-05  0.00082619877
-Loop time of 0.122922 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00116399 on 1 procs for 100 steps with 3 atoms
 
-Performance: 35144210.362 fs/day, 0.000 hours/fs, 813.523 timesteps/s, 2.441 katom-step/s
+Performance: 3711359336.904 fs/day, 0.000 hours/fs, 85911.096 timesteps/s, 257.733 katom-step/s
-70.1% CPU use with 1 MPI tasks x no OpenMP threads
+89.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 1.1593e-05 | 1.1593e-05 | 1.1593e-05 |   0.0 |  0.01
+Neigh   | 1.292e-06  | 1.292e-06  | 1.292e-06  |   0.0 |  0.11
-Comm    | 9.2183e-05 | 9.2183e-05 | 9.2183e-05 |   0.0 |  0.07
+Comm    | 1.2305e-05 | 1.2305e-05 | 1.2305e-05 |   0.0 |  1.06
-Output  | 0.023243   | 0.023243   | 0.023243   |   0.0 | 18.91
+Output  | 0.00018105 | 0.00018105 | 0.00018105 |   0.0 | 15.55
-Modify  | 0.099386   | 0.099386   | 0.099386   |   0.0 | 80.85
+Modify  | 0.00090255 | 0.00090255 | 0.00090255 |   0.0 | 77.54
-Other   |            | 0.0001896  |            |       |  0.15
+Other   |            | 6.68e-05   |            |       |  5.74
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -234,3 +235,4 @@ Total # of neighbors = 0
 Ave neighs/atom = 0
 Neighbor list builds = 33
 Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.1

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 1
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              1.3661449e-08  0.0009918329 
@@ -200,20 +201,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
         98   2.5769956e-05  1.780703e-05   0.00083221292
         99   2.624134e-05   1.8141862e-05  0.00082913227
        100   2.6731735e-05  1.8457846e-05  0.00082619877
-Loop time of 0.122878 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.0011782 on 1 procs for 100 steps with 3 atoms
 
-Performance: 35156789.883 fs/day, 0.000 hours/fs, 813.815 timesteps/s, 2.441 katom-step/s
+Performance: 3666606971.137 fs/day, 0.000 hours/fs, 84875.161 timesteps/s, 254.625 katom-step/s
-46.7% CPU use with 1 MPI tasks x no OpenMP threads
+88.4% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 1.9787e-05 | 1.9787e-05 | 1.9787e-05 |   0.0 |  0.02
+Neigh   | 1.773e-06  | 1.773e-06  | 1.773e-06  |   0.0 |  0.15
-Comm    | 9.2033e-05 | 9.2033e-05 | 9.2033e-05 |   0.0 |  0.07
+Comm    | 1.4979e-05 | 1.4979e-05 | 1.4979e-05 |   0.0 |  1.27
-Output  | 0.0022584  | 0.0022584  | 0.0022584  |   0.0 |  1.84
+Output  | 0.00021888 | 0.00021888 | 0.00021888 |   0.0 | 18.58
-Modify  | 0.12033    | 0.12033    | 0.12033    |   0.0 | 97.93
+Modify  | 0.00086503 | 0.00086503 | 0.00086503 |   0.0 | 73.42
-Other   |            | 0.0001755  |            |       |  0.14
+Other   |            | 7.754e-05  |            |       |  6.58
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -226,3 +227,4 @@ Total # of neighbors = 0
 Ave neighs/atom = 0
 Neighbor list builds = 44
 Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.2

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 2
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              1.3661449e-08  0.0009918329 
@@ -200,20 +201,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
         98   1.8568337e-05  1.780703e-05   0.00083221292
         99   1.9188379e-05  1.8141862e-05  0.00082913227
        100   1.9789011e-05  1.8457846e-05  0.00082619877
-Loop time of 0.112003 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00116163 on 1 procs for 100 steps with 3 atoms
 
-Performance: 38570373.396 fs/day, 0.000 hours/fs, 892.833 timesteps/s, 2.678 katom-step/s
+Performance: 3718915419.639 fs/day, 0.000 hours/fs, 86086.005 timesteps/s, 258.258 katom-step/s
-52.7% CPU use with 1 MPI tasks x no OpenMP threads
+89.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 1.4356e-05 | 1.4356e-05 | 1.4356e-05 |   0.0 |  0.01
+Neigh   | 1.582e-06  | 1.582e-06  | 1.582e-06  |   0.0 |  0.14
-Comm    | 9.7936e-05 | 9.7936e-05 | 9.7936e-05 |   0.0 |  0.09
+Comm    | 1.3306e-05 | 1.3306e-05 | 1.3306e-05 |   0.0 |  1.15
-Output  | 0.0017373  | 0.0017373  | 0.0017373  |   0.0 |  1.55
+Output  | 0.00017996 | 0.00017996 | 0.00017996 |   0.0 | 15.49
-Modify  | 0.10997    | 0.10997    | 0.10997    |   0.0 | 98.19
+Modify  | 0.00090771 | 0.00090771 | 0.00090771 |   0.0 | 78.14
-Other   |            | 0.0001804  |            |       |  0.16
+Other   |            | 5.907e-05  |            |       |  5.09
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -226,3 +227,4 @@ Total # of neighbors = 0
 Ave neighs/atom = 0
 Neighbor list builds = 41
 Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 3
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              1.3661449e-08  0.0009918329 
@@ -200,20 +201,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
         98   2.5288512e-05  1.780703e-05   0.00083221292
         99   2.5384836e-05  1.8141862e-05  0.00082913227
        100   2.5401412e-05  1.8457846e-05  0.00082619877
-Loop time of 0.122921 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00116067 on 1 procs for 100 steps with 3 atoms
 
-Performance: 35144393.915 fs/day, 0.000 hours/fs, 813.528 timesteps/s, 2.441 katom-step/s
+Performance: 3721997782.310 fs/day, 0.000 hours/fs, 86157.356 timesteps/s, 258.472 katom-step/s
-88.8% CPU use with 1 MPI tasks x no OpenMP threads
+88.3% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 1.5885e-05 | 1.5885e-05 | 1.5885e-05 |   0.0 |  0.01
+Neigh   | 1.441e-06  | 1.441e-06  | 1.441e-06  |   0.0 |  0.12
-Comm    | 9.4707e-05 | 9.4707e-05 | 9.4707e-05 |   0.0 |  0.08
+Comm    | 1.2111e-05 | 1.2111e-05 | 1.2111e-05 |   0.0 |  1.04
-Output  | 0.0027076  | 0.0027076  | 0.0027076  |   0.0 |  2.20
+Output  | 0.00018148 | 0.00018148 | 0.00018148 |   0.0 | 15.64
-Modify  | 0.11993    | 0.11993    | 0.11993    |   0.0 | 97.57
+Modify  | 0.0009054  | 0.0009054  | 0.0009054  |   0.0 | 78.01
-Other   |            | 0.0001738  |            |       |  0.14
+Other   |            | 6.023e-05  |            |       |  5.19
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -226,3 +227,4 @@ Total # of neighbors = 0
 Ave neighs/atom = 0
 Neighbor list builds = 42
 Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++

@@ -0,0 +1,2 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
+Running on 4 partitions of processors

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.0

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 0
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -99,11 +100,11 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
 Fix pimd/nvt -P/(beta^2 * hbar^2) =       -2.2139311e-05 (kcal/mol/A^2)
 
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              0              0.00024794798
@@ -207,20 +208,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
         98   7.4842314e-06  1.8940408e-06  0.0002348915 
         99   7.622805e-06   1.9289045e-06  0.00023466684
        100   7.76221e-06    1.9639756e-06  0.00023444136
-Loop time of 0.00940749 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00193128 on 1 procs for 100 steps with 3 atoms
 
-Performance: 459208566.791 fs/day, 0.000 hours/fs, 10629.828 timesteps/s, 31.889 katom-step/s
+Performance: 2236858456.568 fs/day, 0.000 hours/fs, 51779.131 timesteps/s, 155.337 katom-step/s
-90.3% CPU use with 1 MPI tasks x no OpenMP threads
+36.5% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 8.466e-06  | 8.466e-06  | 8.466e-06  |   0.0 |  0.09
+Neigh   | 1.454e-06  | 1.454e-06  | 1.454e-06  |   0.0 |  0.08
-Comm    | 7.8365e-05 | 7.8365e-05 | 7.8365e-05 |   0.0 |  0.83
+Comm    | 2.3033e-05 | 2.3033e-05 | 2.3033e-05 |   0.0 |  1.19
-Output  | 0.0012482  | 0.0012482  | 0.0012482  |   0.0 | 13.27
+Output  | 0.00030824 | 0.00030824 | 0.00030824 |   0.0 | 15.96
-Modify  | 0.0079193  | 0.0079193  | 0.0079193  |   0.0 | 84.18
+Modify  | 0.001541   | 0.001541   | 0.001541   |   0.0 | 79.79
-Other   |            | 0.0001532  |            |       |  1.63
+Other   |            | 5.754e-05  |            |       |  2.98
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.1

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 1
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              0              0.00024796164
@@ -205,20 +206,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
         98   7.3002707e-06  1.8531354e-06  0.00024148118
         99   7.4315008e-06  1.88617e-06    0.00024137268
        100   7.563358e-06   1.9193596e-06  0.00024126398
-Loop time of 0.00941353 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00190888 on 1 procs for 100 steps with 3 atoms
 
-Performance: 458913876.206 fs/day, 0.000 hours/fs, 10623.006 timesteps/s, 31.869 katom-step/s
+Performance: 2263110719.025 fs/day, 0.000 hours/fs, 52386.822 timesteps/s, 157.160 katom-step/s
-50.9% CPU use with 1 MPI tasks x no OpenMP threads
+0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 8.215e-06  | 8.215e-06  | 8.215e-06  |   0.0 |  0.09
+Neigh   | 2.774e-06  | 2.774e-06  | 2.774e-06  |   0.0 |  0.15
-Comm    | 7.7692e-05 | 7.7692e-05 | 7.7692e-05 |   0.0 |  0.83
+Comm    | 2.3215e-05 | 2.3215e-05 | 2.3215e-05 |   0.0 |  1.22
-Output  | 0.0047662  | 0.0047662  | 0.0047662  |   0.0 | 50.63
+Output  | 0.00042246 | 0.00042246 | 0.00042246 |   0.0 | 22.13
-Modify  | 0.004407   | 0.004407   | 0.004407   |   0.0 | 46.82
+Modify  | 0.0013744  | 0.0013744  | 0.0013744  |   0.0 | 72.00
-Other   |            | 0.0001545  |            |       |  1.64
+Other   |            | 8.601e-05  |            |       |  4.51
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.2

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 2
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              0              0.00024796164
@@ -205,20 +206,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
         98   7.1356907e-06  1.7335027e-06  0.0002297417 
         99   7.2605738e-06  1.7643404e-06  0.00022943234
        100   7.3859169e-06  1.7952968e-06  0.00022912226
-Loop time of 0.00941372 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00195857 on 1 procs for 100 steps with 3 atoms
 
-Performance: 458904516.311 fs/day, 0.000 hours/fs, 10622.790 timesteps/s, 31.868 katom-step/s
+Performance: 2205688634.372 fs/day, 0.000 hours/fs, 51057.607 timesteps/s, 153.173 katom-step/s
-24.7% CPU use with 1 MPI tasks x no OpenMP threads
+39.2% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 8.785e-06  | 8.785e-06  | 8.785e-06  |   0.0 |  0.09
+Neigh   | 1.602e-06  | 1.602e-06  | 1.602e-06  |   0.0 |  0.08
-Comm    | 7.9921e-05 | 7.9921e-05 | 7.9921e-05 |   0.0 |  0.85
+Comm    | 1.6951e-05 | 1.6951e-05 | 1.6951e-05 |   0.0 |  0.87
-Output  | 0.0071119  | 0.0071119  | 0.0071119  |   0.0 | 75.55
+Output  | 0.00032627 | 0.00032627 | 0.00032627 |   0.0 | 16.66
-Modify  | 0.0020558  | 0.0020558  | 0.0020558  |   0.0 | 21.84
+Modify  | 0.0015486  | 0.0015486  | 0.0015486  |   0.0 | 79.07
-Other   |            | 0.0001572  |            |       |  1.67
+Other   |            | 6.514e-05  |            |       |  3.33
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 3
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              0              0.00024796164
@@ -205,20 +206,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
         98   7.2937187e-06  1.8407787e-06  0.00023702765
         99   7.4250201e-06  1.8736806e-06  0.00023685186
        100   7.5569619e-06  1.9067398e-06  0.00023667607
-Loop time of 0.00939597 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00197094 on 1 procs for 100 steps with 3 atoms
 
-Performance: 459771778.655 fs/day, 0.000 hours/fs, 10642.865 timesteps/s, 31.929 katom-step/s
+Performance: 2191851993.165 fs/day, 0.000 hours/fs, 50737.315 timesteps/s, 152.212 katom-step/s
-25.2% CPU use with 1 MPI tasks x no OpenMP threads
+37.5% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 8.404e-06  | 8.404e-06  | 8.404e-06  |   0.0 |  0.09
+Neigh   | 1.652e-06  | 1.652e-06  | 1.652e-06  |   0.0 |  0.08
-Comm    | 8.6872e-05 | 8.6872e-05 | 8.6872e-05 |   0.0 |  0.92
+Comm    | 1.7965e-05 | 1.7965e-05 | 1.7965e-05 |   0.0 |  0.91
-Output  | 0.0071309  | 0.0071309  | 0.0071309  |   0.0 | 75.89
+Output  | 0.00036011 | 0.00036011 | 0.00036011 |   0.0 | 18.27
-Modify  | 0.0020085  | 0.0020085  | 0.0020085  |   0.0 | 21.38
+Modify  | 0.0015231  | 0.0015231  | 0.0015231  |   0.0 | 77.28
-Other   |            | 0.0001612  |            |       |  1.72
+Other   |            | 6.806e-05  |            |       |  3.45
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/SPIN/read_restart/in.spin.read_data

@@ -7,6 +7,7 @@ atom_style 	spin
 # necessary for the serial algorithm (sametag)
 atom_modify     map array
 read_data       Norm_randXY_8x8x32.data
+replicate       1 1 2
 
 mass            1 58.93
 
@@ -40,6 +41,6 @@ thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
 thermo_modify   format float %20.15g
 
 compute         outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump            1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
+#dump_modify     1 sort id
 run             100

examples/SPIN/read_restart/in.spin.write_restart

@@ -18,7 +18,7 @@ create_atoms 	1 box
 
 mass            1 58.93
 
-set 		group all spin/random 31 1.72
+set             group all spin/atom/random 31 1.72
 
 pair_style      spin/exchange 4.0
 pair_coeff      * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
@@ -48,7 +48,7 @@ thermo_style    custom step time v_magnorm pe v_emag temp etotal
 thermo          100
 
 compute         outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
+#dump_modify     100 sort id
 run             1000
 write_restart   restart_hcp_cobalt.equil

examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1

@@ -0,0 +1,136 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+units           metal
+dimension       3
+boundary        p p p
+
+atom_style      spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+read_data       Norm_randXY_8x8x32.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (15 28.32 13.68)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1024 atoms
+  reading velocities ...
+  1024 velocities
+  read_data CPU = 0.004 seconds
+replicate       1 1 2
+Replication is creating a 1x1x2 = 2 times larger system...
+  orthogonal box = (0 0 0) to (15 28.32 27.36)
+  1 by 1 by 1 MPI processor grid
+  2048 atoms
+  replicate CPU = 0.001 seconds
+
+mass            1 58.93
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff      * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor        1.0 bin
+neigh_modify    every 1 check no delay 0
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# define outputs and computes
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo          20
+thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump            1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump_modify     1 sort id
+run             100
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.499539
+  ghost atom cutoff = 7.499539
+  binsize = 3.7497695, bins = 5 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 7.499539
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 9.082 | 9.082 | 9.082 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag         v_tmag          Temp          TotEng    
+         0                     0     0.99566943155533     116726.359107918    -852.392312873949     34.9207785637842                    0     116726.359107918
+        20                 0.002    0.995669416541629     70905.5692189811    -849.222504107045      34.647400481739     172820.122486868     116632.998844426
+        40                 0.004    0.995669401356638     71221.2391274615    -848.368415908416     34.9759984641547     171555.103338675     116613.950357609
+        60                 0.006    0.995669394598344     69647.7523345612    -845.585158124559      36.100016238044     177502.681559427     116614.166097826
+        80                 0.008    0.995669395756676     107415.560454437    -846.200871523815     37.9775024824566     35031.4099604677     116684.714477685
+       100                  0.01    0.995669403283478     63849.6798250643    -836.341677782106      39.680777051272     199492.565587335     116634.518317396
+Loop time of 2.97847 on 1 procs for 100 steps with 2048 atoms
+
+Performance: 0.290 ns/day, 82.735 hours/ns, 33.574 timesteps/s, 68.760 katom-step/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.0361     | 1.0361     | 1.0361     |   0.0 | 34.79
+Neigh   | 0.78559    | 0.78559    | 0.78559    |   0.0 | 26.38
+Comm    | 0.013262   | 0.013262   | 0.013262   |   0.0 |  0.45
+Output  | 0.00026908 | 0.00026908 | 0.00026908 |   0.0 |  0.01
+Modify  | 1.1415     | 1.1415     | 1.1415     |   0.0 | 38.33
+Other   |            | 0.001761   |            |       |  0.06
+
+Nlocal:           2048 ave        2048 max        2048 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           7952 ave        7952 max        7952 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         314944 ave      314944 max      314944 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       629888 ave      629888 max      629888 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 629888
+Ave neighs/atom = 307.5625
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:03

examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4

@@ -0,0 +1,136 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+units           metal
+dimension       3
+boundary        p p p
+
+atom_style      spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+read_data       Norm_randXY_8x8x32.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (15 28.32 13.68)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1024 atoms
+  reading velocities ...
+  1024 velocities
+  read_data CPU = 0.004 seconds
+replicate       1 1 2
+Replication is creating a 1x1x2 = 2 times larger system...
+  orthogonal box = (0 0 0) to (15 28.32 27.36)
+  1 by 2 by 2 MPI processor grid
+  2048 atoms
+  replicate CPU = 0.002 seconds
+
+mass            1 58.93
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff      * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor        1.0 bin
+neigh_modify    every 1 check no delay 0
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# define outputs and computes
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo          20
+thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump            1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump_modify     1 sort id
+run             100
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.499539
+  ghost atom cutoff = 7.499539
+  binsize = 3.7497695, bins = 5 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 7.499539
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.812 | 5.812 | 5.812 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag         v_tmag          Temp          TotEng    
+         0                     0    0.995669431555328     116726.359107923     -852.39231287395     34.9207785637843                    0     116726.359107923
+        20                 0.002    0.995669419512638     70905.5692199804    -849.222502855646     34.6474282239503     172820.122483292     116632.998844479
+        40                 0.004    0.995669419108591     71221.2391285209    -848.368412494784       34.97611050919     171555.103335676     116613.950357875
+        60                 0.006     0.99566940895435     69647.7523345112    -845.585157291247     36.1001312564486     177502.681560664     116614.166098104
+        80                 0.008    0.995669417344697     107415.560454912    -846.200874451992     37.9776090859263     35031.4099596403     116684.714477941
+       100                  0.01    0.995669427709463     63849.6798245944    -836.341678212079     39.6809090980074     199492.565591024     116634.518317902
+Loop time of 0.991506 on 4 procs for 100 steps with 2048 atoms
+
+Performance: 0.871 ns/day, 27.542 hours/ns, 100.857 timesteps/s, 206.554 katom-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    | 0.31016    | 0.31287    | 0.31496    |   0.3 | 31.56
+Neigh   | 0.21999    | 0.22957    | 0.23793    |   1.7 | 23.15
+Comm    | 0.015231   | 0.025975   | 0.036137   |   6.0 |  2.62
+Output  | 0.00012037 | 0.00014855 | 0.0001849  |   0.0 |  0.01
+Modify  | 0.4213     | 0.42166    | 0.42201    |   0.0 | 42.53
+Other   |            | 0.001272   |            |       |  0.13
+
+Nlocal:            512 ave         521 max         503 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:           4112 ave        4121 max        4103 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:          78736 ave       80265 max       77207 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+FullNghs:       157472 ave      160276 max      154668 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 629888
+Ave neighs/atom = 307.5625
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:01

examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1

@@ -0,0 +1,135 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# start a spin-lattice simulation from a data file
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+read_restart    restart_hcp_cobalt.equil
+Reading restart file ...
+  restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025
+  restoring atom style spin from restart
+  orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  1 by 1 by 1 MPI processor grid
+  restoring pair style spin/exchange from restart
+  500 atoms
+  read_restart CPU = 0.000 seconds
+
+# setting mass, mag. moments, and interactions
+
+mass            1 58.93
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff      * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor        1.0 bin
+neigh_modify    every 1 check no delay 0
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# define outputs
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo          20
+thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run             100
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.499539
+  ghost atom cutoff = 7.499539
+  binsize = 3.7497695, bins = 4 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 7.499539
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
+Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.255 | 5.255 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag         v_tmag          Temp          TotEng    
+      1000                   0.1   0.0932563992120983    -2200.23506043127    -5.23510819573568      2608.1272233749                    0    -2200.23506043127
+      1020                 0.102   0.0932564226983496    -2200.24431693921    -5.24438874766875     2636.89284253705    0.143502110493468    -2200.23506093651
+      1040                 0.104   0.0932564330551733    -2200.27026761331    -5.27068764778909     2646.09012775508    0.545814389665464    -2200.23506214178
+      1060                 0.106   0.0932564065525508    -2200.30841491752    -5.31025431862422     2627.26990645217     1.13721564075693    -2200.23506358487
+      1080                 0.108   0.0932563850278094    -2200.35339675793    -5.35874497582981     2585.24230543411     1.83458183455181    -2200.23506473927
+      1100                  0.11   0.0932563977118321    -2200.40087596139    -5.41289411193204     2540.00857034711      2.5706738278606    -2200.23506541119
+Loop time of 0.473574 on 1 procs for 100 steps with 500 atoms
+
+Performance: 1.824 ns/day, 13.155 hours/ns, 211.160 timesteps/s, 105.580 katom-step/s
+98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.12025    | 0.12025    | 0.12025    |   0.0 | 25.39
+Neigh   | 0.14912    | 0.14912    | 0.14912    |   0.0 | 31.49
+Comm    | 0.0047587  | 0.0047587  | 0.0047587  |   0.0 |  1.00
+Output  | 0.07234    | 0.07234    | 0.07234    |   0.0 | 15.28
+Modify  | 0.12645    | 0.12645    | 0.12645    |   0.0 | 26.70
+Other   |            | 0.0006494  |            |       |  0.14
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           2534 ave        2534 max        2534 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          36500 ave       36500 max       36500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:        73000 ave       73000 max       73000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 73000
+Ave neighs/atom = 146
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:00

examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4

@@ -0,0 +1,136 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# start a spin-lattice simulation from a data file
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+read_restart    restart_hcp_cobalt.equil
+Reading restart file ...
+  restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025
+WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:628)
+  restoring atom style spin from restart
+  orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  1 by 2 by 2 MPI processor grid
+  restoring pair style spin/exchange from restart
+  500 atoms
+  read_restart CPU = 0.001 seconds
+
+# setting mass, mag. moments, and interactions
+
+mass            1 58.93
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff      * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor        1.0 bin
+neigh_modify    every 1 check no delay 0
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# define outputs
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo          20
+thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run             100
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.499539
+  ghost atom cutoff = 7.499539
+  binsize = 3.7497695, bins = 4 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 7.499539
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
+Per MPI rank memory allocation (min/avg/max) = 5.188 | 5.188 | 5.188 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag         v_tmag          Temp          TotEng    
+      1000                   0.1   0.0932563992120983    -2200.23506043087    -5.23510819573568      2608.1272233749                    0    -2200.23506043087
+      1020                 0.102   0.0932564663999882    -2200.24431693996    -5.24438874845296     2636.89226887198     0.14350212264756    -2200.23506093648
+      1040                 0.104   0.0932565837400281    -2200.27026761822    -5.27068765273516     2646.08966888271    0.545814465748645    -2200.23506214179
+      1060                 0.106   0.0932567073488227    -2200.30841492456    -5.31025432590717     2627.27001685206     1.13721574991944    -2200.23506358486
+      1080                 0.108   0.0932567401022577    -2200.35339675946    -5.35874497805351     2585.24242001276     1.83458185842719    -2200.23506473925
+      1100                  0.11   0.0932566884738387     -2200.4008759633    -5.41289411525345     2540.00813568378     2.57067385759474    -2200.23506541119
+Loop time of 0.180477 on 4 procs for 100 steps with 500 atoms
+
+Performance: 4.787 ns/day, 5.013 hours/ns, 554.088 timesteps/s, 277.044 katom-step/s
+97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.033968   | 0.034363   | 0.035109   |   0.2 | 19.04
+Neigh   | 0.035043   | 0.03728    | 0.040013   |   0.9 | 20.66
+Comm    | 0.0049574  | 0.0073867  | 0.0089549  |   1.7 |  4.09
+Output  | 0.021087   | 0.023594   | 0.026417   |   1.3 | 13.07
+Modify  | 0.074785   | 0.07749    | 0.079892   |   0.7 | 42.94
+Other   |            | 0.0003627  |            |       |  0.20
+
+Nlocal:            125 ave         136 max         117 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost:           1387 ave        1395 max        1376 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs:           9125 ave        9972 max        8559 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+FullNghs:        18250 ave       19856 max       17082 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+
+Total # of neighbors = 73000
+Ave neighs/atom = 146
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:00

examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1

@@ -0,0 +1,142 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# fcc cobalt in a 3d periodic box
+
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+lattice         hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  create_atoms CPU = 0.000 seconds
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass            1 58.93
+
+set             group all spin/atom/random 31 1.72
+Setting atom values ...
+  500 settings made for spin/atom/random
+
+pair_style      spin/exchange 4.0
+pair_coeff      * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 100.0 0.01 21
+
+fix             3 all nve/spin lattice frozen
+timestep        0.0001
+
+# compute and output options
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm pe v_emag temp etotal
+thermo          100
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump_modify     100 sort id
+run             1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 10 steps, delay = 20 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.1
+  ghost atom cutoff = 4.1
+  binsize = 2.05, bins = 7 11 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.78 | 4.78 | 4.78 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag          Temp          TotEng    
+         0   0              0.076558814    0.89911794     0.89911794     0              0.89911794   
+       100   0.01           0.077627966    0.36694275     0.36694275     0              0.36694275   
+       200   0.02           0.076678387   -0.20241504    -0.20241504     0             -0.20241504   
+       300   0.03           0.079174207   -0.67593525    -0.67593525     0             -0.67593525   
+       400   0.04           0.085031074   -1.5172826     -1.5172826      0             -1.5172826    
+       500   0.05           0.087026279   -2.042653      -2.042653       0             -2.042653     
+       600   0.06           0.087064628   -2.6297295     -2.6297295      0             -2.6297295    
+       700   0.07           0.089787949   -3.3144767     -3.3144767      0             -3.3144767    
+       800   0.08           0.091698615   -4.028707      -4.028707       0             -4.028707     
+       900   0.09           0.090031988   -4.6007241     -4.6007241      0             -4.6007241    
+      1000   0.1            0.093256399   -5.2351082     -5.2351082      0             -5.2351082    
+Loop time of 0.710555 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 12.160 ns/day, 1.974 hours/ns, 1407.350 timesteps/s, 703.675 katom-step/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.12852    | 0.12852    | 0.12852    |   0.0 | 18.09
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.012387   | 0.012387   | 0.012387   |   0.0 |  1.74
+Output  | 0.00014522 | 0.00014522 | 0.00014522 |   0.0 |  0.02
+Modify  | 0.56835    | 0.56835    | 0.56835    |   0.0 | 79.99
+Other   |            | 0.001145   |            |       |  0.16
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1221 ave        1221 max        1221 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:        10000 ave       10000 max       10000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 10000
+Ave neighs/atom = 20
+Neighbor list builds = 0
+Dangerous builds = 0
+write_restart   restart_hcp_cobalt.equil
+System init for write_restart ...
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Total wall time: 0:00:00

examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4

@@ -0,0 +1,142 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# fcc cobalt in a 3d periodic box
+
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+lattice         hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  create_atoms CPU = 0.001 seconds
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass            1 58.93
+
+set             group all spin/atom/random 31 1.72
+Setting atom values ...
+  500 settings made for spin/atom/random
+
+pair_style      spin/exchange 4.0
+pair_coeff      * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 100.0 0.01 21
+
+fix             3 all nve/spin lattice frozen
+timestep        0.0001
+
+# compute and output options
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm pe v_emag temp etotal
+thermo          100
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump_modify     100 sort id
+run             1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 10 steps, delay = 20 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.1
+  ghost atom cutoff = 4.1
+  binsize = 2.05, bins = 7 11 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.732 | 4.732 | 4.733 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag          Temp          TotEng    
+         0   0              0.076558814    0.89911794     0.89911794     0              0.89911794   
+       100   0.01           0.078299852    0.44131103     0.44131103     0              0.44131103   
+       200   0.02           0.081260369   -0.2174146     -0.2174146      0             -0.2174146    
+       300   0.03           0.081195064   -0.87039697    -0.87039697     0             -0.87039697   
+       400   0.04           0.087298284   -1.7069593     -1.7069593      0             -1.7069593    
+       500   0.05           0.087663192   -2.1882865     -2.1882865      0             -2.1882865    
+       600   0.06           0.091713114   -2.926766      -2.926766       0             -2.926766     
+       700   0.07           0.093779218   -3.3532704     -3.3532704      0             -3.3532704    
+       800   0.08           0.097960251   -3.9343481     -3.9343481      0             -3.9343481    
+       900   0.09           0.10193598    -4.7944099     -4.7944099      0             -4.7944099    
+      1000   0.1            0.10832963    -5.3823924     -5.3823924      0             -5.3823924    
+Loop time of 0.40066 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 21.564 ns/day, 1.113 hours/ns, 2495.885 timesteps/s, 1.248 Matom-step/s
+97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.032435   | 0.033013   | 0.033957   |   0.3 |  8.24
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.016106   | 0.016898   | 0.017915   |   0.5 |  4.22
+Output  | 0.00012331 | 0.00013523 | 0.00016852 |   0.0 |  0.03
+Modify  | 0.34913    | 0.34974    | 0.35017    |   0.1 | 87.29
+Other   |            | 0.0008755  |            |       |  0.22
+
+Nlocal:            125 ave         125 max         125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:          597.5 ave         600 max         595 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:         2500 ave        2500 max        2500 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 10000
+Ave neighs/atom = 20
+Neighbor list builds = 0
+Dangerous builds = 0
+write_restart   restart_hcp_cobalt.equil
+System init for write_restart ...
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Total wall time: 0:00:00

examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.1

@@ -1,110 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-dimension 	3
-boundary 	p p p
-
-atom_style 	spin
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-read_data 	Norm_randXY_8x8x32.data
-  orthogonal box = (0 0 0) to (28.32 28.32 113.28)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  8192 atoms
-  read_data CPU = 0.022048 secs
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice moving
-timestep	0.0001
-
-# define outputs and computes
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          20
-thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 8 8 31
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 19.99 | 19.99 | 19.99 Mbytes
-Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng 
-       0                    0   0.0177864461018737    -36558.7284872918    -661.829206399896       1274.398774669                    0    -36558.7284872918 
-      20                0.002   0.0177864377256184    -36558.7389378387    -661.839683504936     1259.94171978912  0.00986992693139795    -36558.7284878577 
-      40                0.004    0.017786472977471    -36558.7684525639    -661.869582914286     1224.05894016152   0.0377451568363827    -36558.7284891299 
-      60                0.006   0.0177865119543331    -36558.8126238543    -661.915330492427     1184.24369688088   0.0794631076347515     -36558.728490712 
-      80                0.008   0.0177865172048059    -36558.8659242367    -661.972562482488     1152.05459929593    0.129803482511904    -36558.7284922233 
-     100                 0.01   0.0177865063752424    -36558.9229549739    -662.037138807935     1129.51470280479    0.183667498513087    -36558.7284933644 
-Loop time of 14.3276 on 1 procs for 100 steps with 8192 atoms
-
-Performance: 0.060 ns/day, 397.988 hours/ns, 6.980 timesteps/s
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 4.0409     | 4.0409     | 4.0409     |   0.0 | 28.20
-Neigh   | 3.6219     | 3.6219     | 3.6219     |   0.0 | 25.28
-Comm    | 0.055327   | 0.055327   | 0.055327   |   0.0 |  0.39
-Output  | 2.4259     | 2.4259     | 2.4259     |   0.0 | 16.93
-Modify  | 4.1688     | 4.1688     | 4.1688     |   0.0 | 29.10
-Other   |            | 0.01477    |            |       |  0.10
-
-Nlocal:    8192 ave 8192 max 8192 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    14621 ave 14621 max 14621 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    573440 ave 573440 max 573440 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  1.14688e+06 ave 1.14688e+06 max 1.14688e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1146880
-Ave neighs/atom = 140
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:14

examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.4

@@ -1,110 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-dimension 	3
-boundary 	p p p
-
-atom_style 	spin
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-read_data 	Norm_randXY_8x8x32.data
-  orthogonal box = (0 0 0) to (28.32 28.32 113.28)
-  1 by 1 by 4 MPI processor grid
-  reading atoms ...
-  8192 atoms
-  read_data CPU = 0.013634 secs
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice moving
-timestep	0.0001
-
-# define outputs and computes
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          20
-thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 8 8 31
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 8.961 | 9.047 | 9.29 Mbytes
-Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng 
-       0                    0   0.0177864461018739    -36558.7284872997    -661.829206399894       1274.398774669                    0    -36558.7284872997 
-      20                0.002   0.0177863981273124    -36558.7389378386    -661.839683504262     1259.94177798388  0.00986992629371963    -36558.7284878582 
-      40                0.004   0.0177864622701489    -36558.7684525586    -661.869582908114     1224.05908191331   0.0377451510479599    -36558.7284891308 
-      60                0.006   0.0177865625037858    -36558.8126238326    -661.915330472361     1184.24389640891   0.0794630890177406      -36558.72849071 
-      80                0.008   0.0177865898045059    -36558.8659241943    -661.972562439245     1152.05483020781    0.129803443061299    -36558.7284922226 
-     100                 0.01    0.017786565190115    -36558.9229549058    -662.037138735432     1129.51495182843    0.183667434061771    -36558.7284933646 
-Loop time of 4.35911 on 4 procs for 100 steps with 8192 atoms
-
-Performance: 0.198 ns/day, 121.086 hours/ns, 22.940 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.0924     | 1.1043     | 1.1117     |   0.7 | 25.33
-Neigh   | 0.93575    | 0.94926    | 0.98325    |   2.0 | 21.78
-Comm    | 0.044663   | 0.088288   | 0.11128    |   8.7 |  2.03
-Output  | 0.64199    | 0.6587     | 0.67226    |   1.4 | 15.11
-Modify  | 1.5412     | 1.5535     | 1.5706     |   0.9 | 35.64
-Other   |            | 0.005046   |            |       |  0.12
-
-Nlocal:    2048 ave 2061 max 2035 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Nghost:    5765 ave 5778 max 5752 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Neighs:    143360 ave 144262 max 142469 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-FullNghs:  286720 ave 288540 max 284900 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 1146880
-Ave neighs/atom = 140
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:04

examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.1

@@ -1,116 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-# start a spin-lattice simulation from a data file
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-read_restart	restart_hcp_cobalt.equil
-WARNING: Restart file used different # of processors: 4 vs. 1 (../read_restart.cpp:736)
-  restoring atom style spin from restart
-  orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 1 by 1 MPI processor grid
-  restoring pair style spin/exchange from restart
-  500 atoms
-  read_restart CPU = 0.00179696 secs
-
-# setting mass, mag. moments, and interactions
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice moving
-timestep	0.0001
-
-# define outputs
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          20
-thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 4 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.422 | 7.422 | 7.422 Mbytes
-Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng 
-    1000                    0    0.108317262557656    -2200.38241212222    -5.38245988668244      2538.4247868621                    0    -2200.38241212222 
-    1020                0.002    0.108317318495042    -2200.39172132133    -5.39179331134703     2513.42968070374    0.144319963844279    -2200.38241256643 
-    1040                0.004    0.108317415558744    -2200.41811580407      -5.418541526637     2478.87571728648    0.553516420254567    -2200.38241354532 
-    1060                0.006    0.108317473592946    -2200.45801216332    -5.45990062771403     2449.77257658726     1.17203792179707    -2200.38241476526 
-    1080                0.008    0.108317450745396     -2200.5068824087    -5.51245983698347     2427.25022669715     1.92968606059505     -2200.3824160902 
-    1100                 0.01    0.108317381572202    -2200.55976028827    -5.57250071024394     2400.86131889957     2.74946927499959    -2200.38241728649 
-Loop time of 0.954493 on 1 procs for 100 steps with 500 atoms
-
-Performance: 0.905 ns/day, 26.514 hours/ns, 104.768 timesteps/s
-100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.27043    | 0.27043    | 0.27043    |   0.0 | 28.33
-Neigh   | 0.26148    | 0.26148    | 0.26148    |   0.0 | 27.40
-Comm    | 0.0071123  | 0.0071123  | 0.0071123  |   0.0 |  0.75
-Output  | 0.14169    | 0.14169    | 0.14169    |   0.0 | 14.84
-Modify  | 0.2726     | 0.2726     | 0.2726     |   0.0 | 28.56
-Other   |            | 0.001178   |            |       |  0.12
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2534 ave 2534 max 2534 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    36500 ave 36500 max 36500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  73000 ave 73000 max 73000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 73000
-Ave neighs/atom = 146
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:01

examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.4

@@ -1,115 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-# start a spin-lattice simulation from a data file
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-read_restart	restart_hcp_cobalt.equil
-  restoring atom style spin from restart
-  orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 2 by 2 MPI processor grid
-  restoring pair style spin/exchange from restart
-  500 atoms
-  read_restart CPU = 0.00173593 secs
-
-# setting mass, mag. moments, and interactions
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice moving
-timestep	0.0001
-
-# define outputs
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          20
-thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 4 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.324 | 7.324 | 7.324 Mbytes
-Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng 
-    1000                    0    0.108317262557656    -2200.38241212182    -5.38245988668244      2538.4247868621                    0    -2200.38241212182 
-    1020                0.002    0.108317316216432    -2200.39172132147    -5.39179331147409     2513.42945241007     0.14431996581917    -2200.38241256644 
-    1040                0.004    0.108317347939802    -2200.41811580574    -5.41854152831072     2478.87544274124    0.553516446104432    -2200.38241354532 
-    1060                0.006    0.108317342440309    -2200.45801216927    -5.45990063373049     2449.77218633122     1.17203801398165    -2200.38241476526 
-    1080                0.008    0.108317320345284    -2200.50688241767    -5.51245984623572      2427.2497145488     1.92968619968329     -2200.3824160902 
-    1100                 0.01     0.10831728372281    -2200.55976028296    -5.57250070536486     2400.86059511731     2.74946919265255    -2200.38241728649 
-Loop time of 0.405615 on 4 procs for 100 steps with 500 atoms
-
-Performance: 2.130 ns/day, 11.267 hours/ns, 246.539 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.075661   | 0.076798   | 0.077343   |   0.2 | 18.93
-Neigh   | 0.063154   | 0.064974   | 0.066991   |   0.5 | 16.02
-Comm    | 0.012538   | 0.013787   | 0.015151   |   0.8 |  3.40
-Output  | 0.039155   | 0.040842   | 0.042502   |   0.6 | 10.07
-Modify  | 0.20709    | 0.20883    | 0.21036    |   0.3 | 51.49
-Other   |            | 0.0003826  |            |       |  0.09
-
-Nlocal:    125 ave 127 max 122 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Nghost:    1387 ave 1390 max 1385 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Neighs:    9125 ave 9272 max 8945 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-FullNghs:  18250 ave 18542 max 17812 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-
-Total # of neighbors = 73000
-Ave neighs/atom = 146
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:00

examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.1

@@ -1,120 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-# fcc cobalt in a 3d periodic box
-
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	hcp 2.5071
-Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  create_atoms CPU = 0.000952005 secs
-
-# setting mass, mag. moments, and interactions for cobalt
-
-mass		1 58.93
-
-set 		group all spin/random 31 1.72
-  500 settings made for spin/random
-
-pair_style	spin/exchange 4.0
-pair_coeff 	* * exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 100.0 0.01 21
-
-fix 		3 all nve/spin lattice frozen
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm pe v_emag temp etotal
-thermo          100
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		1000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 4.1
-  ghost atom cutoff = 4.1
-  binsize = 2.05, bins = 7 11 10
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.947 | 6.947 | 6.947 Mbytes
-Step Time v_magnorm PotEng v_emag Temp TotEng 
-       0            0  0.076558814   0.89911794   0.89911794            0   0.89911794 
-     100         0.01  0.077628154   0.36693917   0.36693917            0   0.36693917 
-     200         0.02  0.076678996  -0.20242315  -0.20242315            0  -0.20242315 
-     300         0.03  0.079174837  -0.67595514  -0.67595514            0  -0.67595514 
-     400         0.04  0.085031632   -1.5172851   -1.5172851            0   -1.5172851 
-     500         0.05   0.08702747   -2.0426628   -2.0426628            0   -2.0426628 
-     600         0.06  0.087066482   -2.6297745   -2.6297745            0   -2.6297745 
-     700         0.07  0.089788894    -3.314538    -3.314538            0    -3.314538 
-     800         0.08  0.091699611   -4.0287043   -4.0287043            0   -4.0287043 
-     900         0.09  0.090038899    -4.600601    -4.600601            0    -4.600601 
-    1000          0.1  0.093257309   -5.2352261   -5.2352261            0   -5.2352261 
-Loop time of 3.30071 on 1 procs for 1000 steps with 500 atoms
-
-Performance: 2.618 ns/day, 9.169 hours/ns, 302.965 timesteps/s
-99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.3844     | 0.3844     | 0.3844     |   0.0 | 11.65
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.019863   | 0.019863   | 0.019863   |   0.0 |  0.60
-Output  | 1.3844     | 1.3844     | 1.3844     |   0.0 | 41.94
-Modify  | 1.5084     | 1.5084     | 1.5084     |   0.0 | 45.70
-Other   |            | 0.00367    |            |       |  0.11
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1221 ave 1221 max 1221 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  10000 ave 10000 max 10000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 10000
-Ave neighs/atom = 20
-Neighbor list builds = 0
-Dangerous builds = 0
-write_restart 	restart_hcp_cobalt.equil
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03

examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.4

@@ -1,120 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-# fcc cobalt in a 3d periodic box
-
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	hcp 2.5071
-Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  create_atoms CPU = 0.000663042 secs
-
-# setting mass, mag. moments, and interactions for cobalt
-
-mass		1 58.93
-
-set 		group all spin/random 31 1.72
-  500 settings made for spin/random
-
-pair_style	spin/exchange 4.0
-pair_coeff 	* * exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 100.0 0.01 21
-
-fix 		3 all nve/spin lattice frozen
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm pe v_emag temp etotal
-thermo          100
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		1000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 4.1
-  ghost atom cutoff = 4.1
-  binsize = 2.05, bins = 7 11 10
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.868 | 6.868 | 6.868 Mbytes
-Step Time v_magnorm PotEng v_emag Temp TotEng 
-       0            0  0.076558814   0.89911794   0.89911794            0   0.89911794 
-     100         0.01  0.078299981   0.44129792   0.44129792            0   0.44129792 
-     200         0.02  0.081260508  -0.21742361  -0.21742361            0  -0.21742361 
-     300         0.03  0.081195603  -0.87041046  -0.87041046            0  -0.87041046 
-     400         0.04  0.087298495   -1.7069519   -1.7069519            0   -1.7069519 
-     500         0.05  0.087663924   -2.1883045   -2.1883045            0   -2.1883045 
-     600         0.06  0.091713683   -2.9267461   -2.9267461            0   -2.9267461 
-     700         0.07  0.093779119    -3.353314    -3.353314            0    -3.353314 
-     800         0.08  0.097960611   -3.9344284   -3.9344284            0   -3.9344284 
-     900         0.09   0.10193463   -4.7944004   -4.7944004            0   -4.7944004 
-    1000          0.1   0.10831726   -5.3824599   -5.3824599            0   -5.3824599 
-Loop time of 1.7839 on 4 procs for 1000 steps with 500 atoms
-
-Performance: 4.843 ns/day, 4.955 hours/ns, 560.569 timesteps/s
-99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.10068    | 0.10749    | 0.11461    |   1.5 |  6.03
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.052378   | 0.062171   | 0.07177    |   2.8 |  3.49
-Output  | 0.4054     | 0.42334    | 0.44025    |   2.0 | 23.73
-Modify  | 1.174      | 1.1893     | 1.2043     |   1.1 | 66.67
-Other   |            | 0.001558   |            |       |  0.09
-
-Nlocal:    125 ave 125 max 125 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    597.5 ave 600 max 595 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  2500 ave 2500 max 2500 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 10000
-Ave neighs/atom = 20
-Neighbor list builds = 0
-Dangerous builds = 0
-write_restart 	restart_hcp_cobalt.equil
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:01

src/.gitignore

@@ -1661,10 +1661,14 @@
 /fix_pimd.h
 /fix_pimd_langevin.cpp
 /fix_pimd_langevin.h
+/fix_pimd_langevin_bosonic.cpp
+/fix_pimd_langevin_bosonic.h
 /fix_alchemy.cpp
 /fix_alchemy.h
 /fix_pimd_nvt.cpp
 /fix_pimd_nvt.h
+/fix_pimd_nvt_bosonic.cpp
+/fix_pimd_nvt_bosonic.h
 /fix_qbmsst.cpp
 /fix_qbmsst.h
 /fix_qtb.cpp

src/AMOEBA/fix_amoeba_bitorsion.cpp

@@ -82,6 +82,7 @@ FixAmoebaBiTorsion::FixAmoebaBiTorsion(LAMMPS *lmp, int narg, char **arg) :
   wd_section = 1;
   respa_level_support = 1;
   ilevel_respa = 0;
+  stores_ids = 1;
 
   MPI_Comm_rank(world,&me);
   MPI_Comm_size(world,&nprocs);

src/AMOEBA/fix_amoeba_pitorsion.cpp

@@ -62,6 +62,7 @@ FixAmoebaPiTorsion::FixAmoebaPiTorsion(LAMMPS *lmp, int narg, char **arg) :
   wd_section = 1;
   respa_level_support = 1;
   ilevel_respa = 0;
+  stores_ids = 1;
 
   MPI_Comm_rank(world,&me);
   MPI_Comm_size(world,&nprocs);

src/BPM/bond_bpm_spring_plastic.cpp

@@ -430,7 +430,7 @@ double BondBPMSpringPlastic::single(int type, double rsq, int i, int j, double &
 {
   if (type <= 0) return 0.0;
 
-  double r0, ep;
+  double r0 = 0.0, ep = 0.0;
   for (int n = 0; n < atom->num_bond[i]; n++) {
     if (atom->bond_atom[i][n] == atom->tag[j]) {
       r0 = fix_bond_history->get_atom_value(i, n, 0);
@@ -471,7 +471,7 @@ double BondBPMSpringPlastic::single(int type, double rsq, int i, int j, double &
   // set single_extra quantities
 
   svector[0] = r0;
-  svector[0] = (1.0 + ep) * r0;
+  svector[1] = (1.0 + ep) * r0;
 
   return 0.0;
 }

src/EXTRA-COMPUTE/compute_stress_mop.cpp

@@ -1117,6 +1117,11 @@ void ComputeStressMop::compute_dihedrals()
         df[1] = sgn * (f1[1] + f3[1]);
         df[2] = sgn * (f1[2] + f3[2]);
       }
+
+      // no if matches
+      else {
+       df[0] = df[1] = df[2] = 0.0;
+      }
       local_contribution[0] += df[0] / area * nktv2p;
       local_contribution[1] += df[1] / area * nktv2p;
       local_contribution[2] += df[2] / area * nktv2p;

src/MACHDYN/fix_smd_tlsph_reference_configuration.cpp

@@ -60,6 +60,7 @@ FixSMD_TLSPH_ReferenceConfiguration::FixSMD_TLSPH_ReferenceConfiguration(LAMMPS
   if (atom->map_style == Atom::MAP_NONE)
     error->all(FLERR, "Pair tlsph with partner list requires an atom map, see atom_modify");
 
+  stores_ids = 1;
   maxpartner = 1;
   npartner = nullptr;
   partner = nullptr;

src/MOLECULE/fix_cmap.cpp

@@ -87,6 +87,7 @@ FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) :
   respa_level_support = 1;
   ilevel_respa = 0;
   eflag_caller = 1;
+  stores_ids = 1;
 
   // allocate memory for CMAP data
 

src/PERI/fix_peri_neigh.cpp

@@ -52,6 +52,7 @@ FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
   restart_global = 1;
   restart_peratom = 1;
   first = 1;
+  stores_ids = 1;
 
   // perform initial allocation of atom-based arrays
   // register with atom class

src/REAXFF/fix_qtpie_reaxff.cpp

@@ -23,6 +23,7 @@
 #include "fix_qtpie_reaxff.h"
 
 #include "atom.h"
+#include "citeme.h"
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
@@ -52,6 +53,19 @@ static constexpr double CONV_TO_EV = 14.4;
 static constexpr double QSUMSMALL = 0.00001;
 static constexpr double ANGSTROM_TO_BOHRRADIUS = 1.8897261259;
 
+static const char cite_fix_qtpie_reax[] =
+  "fix qtpie/reaxff command: \n\n"
+  "@Article{Kritikos20,\n"
+  " author = {E. Kritikos and A. Giusti},\n"
+  " title = {Reactive Molecular Dynamics Investigation of Toluene Oxidation under Electrostatic Fields: Effect of the Modeling of Local Charge Distribution},\n"
+  " journal = {The Journal of Physical Chemistry A},\n"
+  " volume = {124},\n"
+  " number = {51},\n"
+  " pages = {10705--10716},\n"
+  " year = {2020},\n"
+  " publisher = {ACS Publications}\n"
+  "}\n\n";
+
 /* ---------------------------------------------------------------------- */
 
 FixQtpieReaxFF::FixQtpieReaxFF(LAMMPS *lmp, int narg, char **arg) :
@@ -165,6 +179,8 @@ FixQtpieReaxFF::~FixQtpieReaxFF()
 
 void FixQtpieReaxFF::post_constructor()
 {
+  if (lmp->citeme) lmp->citeme->add(cite_fix_qtpie_reax);
+
   grow_arrays(atom->nmax);
   for (int i = 0; i < atom->nmax; i++)
     for (int j = 0; j < nprev; ++j)

src/REAXFF/reaxff_ffield.cpp

@@ -234,6 +234,12 @@ namespace ReaxFF {
           if (lgflag) {
             values = reader.next_values(0);
             ++lineno;
+
+            // if line does not start with a floating point number, i.e. is the start
+            // of the data for the next element, the file does not support lgflag != 0
+            if (!values.matches("^\\s*\\f+\\s*"))
+              THROW_ERROR("ReaxFF potential file is not compatible with 'lgvdw yes'");
+
             CHECK_COLUMNS(2);
             sbp[i].lgcij    = values.next_double();
             sbp[i].lgre     = values.next_double();

src/REPLICA/fix_pimd_langevin.cpp

@@ -113,7 +113,8 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
 
   int seed = -1;
 
-  if (domain->dimension != 3) error->universe_all(FLERR, "Fix pimd/langevin requires a 3d system");
+  if (domain->dimension != 3)
+    error->universe_all(FLERR, fmt::format("Fix {} requires a 3d system", style));
 
   for (int i = 0; i < 6; i++) {
     p_flag[i] = 0;
@@ -127,7 +128,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
       else if (strcmp(arg[i + 1], "pimd") == 0)
         method = PIMD;
       else
-        error->universe_all(FLERR, "Unknown method parameter for fix pimd/langevin");
+        error->universe_all(FLERR, fmt::format("Unknown method parameter for fix {}", style));
     } else if (strcmp(arg[i], "integrator") == 0) {
       if (strcmp(arg[i + 1], "obabo") == 0)
         integrator = OBABO;
@@ -135,8 +136,9 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         integrator = BAOAB;
       else
         error->universe_all(FLERR,
-                            "Unknown integrator parameter for fix pimd/langevin. Only obabo and "
+                            fmt::format("Unknown integrator parameter for fix {}. Only obabo and "
-                            "baoab integrators are supported!");
+                                        "baoab integrators are supported!",
+                                        style));
     } else if (strcmp(arg[i], "ensemble") == 0) {
       if (strcmp(arg[i + 1], "nve") == 0) {
         ensemble = NVE;
@@ -156,15 +158,16 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         pstat_flag = 1;
       } else
         error->universe_all(FLERR,
-                            "Unknown ensemble parameter for fix pimd/langevin. Only nve, nvt, nph, "
+                            fmt::format("Unknown ensemble parameter for fix {}. Only nve, nvt, "
-                            "and npt ensembles are supported!");
+                                        "nph, and npt ensembles are supported!",
+                                        style));
     } else if (strcmp(arg[i], "fmass") == 0) {
       fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (fmass < 0.0 || fmass > np)
-        error->universe_all(FLERR, "Invalid fmass value for fix pimd/langevin");
+        error->universe_all(FLERR, fmt::format("Invalid fmass value for fix {}", style));
     } else if (strcmp(arg[i], "sp") == 0) {
       sp = utils::numeric(FLERR, arg[i + 1], false, lmp);
-      if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd/langevin");
+      if (sp < 0.0) error->universe_all(FLERR, fmt::format("Invalid sp value for fix {}", style));
     } else if (strcmp(arg[i], "fmmode") == 0) {
       if (strcmp(arg[i + 1], "physical") == 0)
         fmmode = PHYSICAL;
@@ -172,8 +175,9 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
         fmmode = NORMAL;
       else
         error->universe_all(FLERR,
-                            "Unknown fictitious mass mode for fix pimd/langevin. Only physical "
+                            fmt::format("Unknown fictitious mass mode for fix {}. Only physical "
-                            "mass and normal mode mass are supported!");
+                                        "mass and normal mode mass are supported!",
+                                        style));
     } else if (strcmp(arg[i], "scale") == 0) {
       if (method == PIMD)
         error->universe_all(
@@ -182,10 +186,11 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
             "scale parameter if you do want to use method pimd.");
       pilescale = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if (pilescale < 0.0)
-        error->universe_all(FLERR, "Invalid PILE_L scale value for fix pimd/langevin");
+        error->universe_all(FLERR, fmt::format("Invalid PILE_L scale value for fix {}", style));
     } else if (strcmp(arg[i], "temp") == 0) {
       temp = utils::numeric(FLERR, arg[i + 1], false, lmp);
-      if (temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd/langevin");
+      if (temp < 0.0)
+        error->universe_all(FLERR, fmt::format("Invalid temp value for fix {}", style));
     } else if (strcmp(arg[i], "lj") == 0) {
       lj_epsilon = utils::numeric(FLERR, arg[i + 1], false, lmp);
       lj_sigma = utils::numeric(FLERR, arg[i + 2], false, lmp);
@@ -207,7 +212,7 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
       } else if (strcmp(arg[i + 1], "BZP") == 0) {
         barostat = BZP;
       } else
-        error->universe_all(FLERR, "Unknown barostat parameter for fix pimd/langevin");
+        error->universe_all(FLERR, fmt::format("Unknown barostat parameter for fix {}", style));
     } else if (strcmp(arg[i], "iso") == 0) {
       pstyle = ISO;
       p_flag[0] = p_flag[1] = p_flag[2] = 1;
@@ -237,7 +242,8 @@ FixPIMDLangevin::FixPIMDLangevin(LAMMPS *lmp, int narg, char **arg) :
       pdim++;
     } else if (strcmp(arg[i], "taup") == 0) {
       tau_p = utils::numeric(FLERR, arg[i + 1], false, lmp);
-      if (tau_p <= 0.0) error->universe_all(FLERR, "Invalid tau_p value for fix pimd/langevin");
+      if (tau_p <= 0.0)
+        error->universe_all(FLERR, fmt::format("Invalid tau_p value for fix {}", style));
     } else if (strcmp(arg[i], "fixcom") == 0) {
       if (strcmp(arg[i + 1], "yes") == 0)
         removecomflag = 1;
@@ -403,6 +409,7 @@ FixPIMDLangevin::~FixPIMDLangevin()
   memory->destroy(tagsend);
   memory->destroy(tagrecv);
   memory->destroy(bufbeads);
+  if (rootworld != MPI_COMM_NULL) MPI_Comm_free(&rootworld);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -422,10 +429,10 @@ int FixPIMDLangevin::setmask()
 void FixPIMDLangevin::init()
 {
   if (atom->map_style == Atom::MAP_NONE)
-    error->all(FLERR, "Fix pimd/langevin requires an atom map, see atom_modify");
+    error->all(FLERR, fmt::format("Fix {} requires an atom map, see atom_modify", style));
 
   if (universe->me == 0 && universe->uscreen)
-    fprintf(universe->uscreen, "Fix pimd/langevin: initializing Path-Integral ...\n");
+    utils::print(universe->uscreen, "Fix {}: initializing Path-Integral ...\n", style);
 
   // prepare the constants
 
@@ -448,8 +455,8 @@ void FixPIMDLangevin::init()
   fbond = _fbond * force->mvv2e;
 
   if ((universe->me == 0) && (universe->uscreen))
-    fprintf(universe->uscreen,
+    utils::print(universe->uscreen, "Fix {}: -P/(beta^2 * hbar^2) = {:20.7e} (kcal/mol/A^2)\n\n",
-            "Fix pimd/langevin: -P/(beta^2 * hbar^2) = %20.7lE (kcal/mol/A^2)\n\n", fbond);
+                 style, fbond);
 
   if (integrator == OBABO) {
     dtf = 0.5 * update->dt * force->ftm2v;
@@ -462,7 +469,7 @@ void FixPIMDLangevin::init()
     dtv2 = dtv * dtv;
     dtv3 = THIRD * dtv2 * dtv * force->ftm2v;
   } else {
-    error->universe_all(FLERR, "Unknown integrator parameter for fix pimd/langevin");
+    error->universe_all(FLERR, fmt::format("Unknown integrator parameter for fix {}", style));
   }
 
   comm_init();
@@ -518,11 +525,15 @@ void FixPIMDLangevin::setup(int vflag)
       nmpimd_transform(bufbeads, x, M_x2xp[universe->iworld]);
   } else if (method == PIMD) {
     prepare_coordinates();
+    if (cmode == SINGLE_PROC)
       spring_force();
+    else if (cmode == MULTI_PROC)
+      error->universe_all(FLERR, "Method pimd only supports a single processor per bead");
   } else {
     error->universe_all(
         FLERR,
-        "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!");
+        fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!",
+                    style));
   }
   collect_xc();
   compute_spring_energy();
@@ -584,7 +595,8 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
     } else {
       error->universe_all(
           FLERR,
-          "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!");
+          fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!",
+                      style));
     }
   } else if (integrator == BAOAB) {
     if (pstat_flag) {
@@ -606,7 +618,8 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
     } else {
       error->universe_all(
           FLERR,
-          "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!");
+          fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!",
+                      style));
     }
     if (tstat_flag) {
       o_step();
@@ -621,12 +634,14 @@ void FixPIMDLangevin::initial_integrate(int /*vflag*/)
     } else {
       error->universe_all(
           FLERR,
-          "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!");
+          fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!",
+                      style));
     }
   } else {
     error->universe_all(FLERR,
-                        "Unknown integrator parameter for fix pimd/langevin. Only obabo and baoab "
+                        fmt::format("Unknown integrator parameter for fix {}. Only obabo and baoab "
-                        "integrators are supported!");
+                                    "integrators are supported!",
+                                    style));
   }
   collect_xc();
 
@@ -668,7 +683,7 @@ void FixPIMDLangevin::final_integrate()
   } else if (integrator == BAOAB) {
 
   } else {
-    error->universe_all(FLERR, "Unknown integrator parameter for fix pimd/langevin");
+    error->universe_all(FLERR, fmt::format("Unknown integrator parameter for fix {}", style));
   }
 }
 
@@ -1042,8 +1057,9 @@ void FixPIMDLangevin::langevin_init()
     c1 = exp(-gamma * update->dt);
   else
     error->universe_all(FLERR,
-                        "Unknown integrator parameter for fix pimd/langevin. Only obabo and "
+                        fmt::format("Unknown integrator parameter for fix {}. Only obabo and baoab "
-                        "baoab integrators are supported!");
+                                    "integrators are supported!",
+                                    style));
 
   c2 = sqrt(1.0 - c1 * c1);    // note that c1 and c2 here only works for the centroid mode.
 
@@ -1065,8 +1081,9 @@ void FixPIMDLangevin::langevin_init()
           c1_k[i] = exp(-1.0 * update->dt / tau_k[i]);
         else
           error->universe_all(FLERR,
-                              "Unknown integrator parameter for fix pimd/langevin. Only obabo and "
+                              fmt::format("Unknown integrator parameter for fix {}. Only obabo and "
-                              "baoab integrators are supported!");
+                                          "baoab integrators are supported!",
+                                          style));
         c2_k[i] = sqrt(1.0 - c1_k[i] * c1_k[i]);
       }
       for (int i = 0; i < np; i++) {
@@ -1417,7 +1434,9 @@ void FixPIMDLangevin::remove_com_motion()
       }
     }
   } else {
-    error->all(FLERR, "Unknown method for fix pimd/langevin. Only nmpimd and pimd are supported!");
+    error->all(
+        FLERR,
+        fmt::format("Unknown method for fix {}. Only nmpimd and pimd are supported!", style));
   }
 }
 
@@ -1548,7 +1567,8 @@ void FixPIMDLangevin::compute_spring_energy()
   } else {
     error->universe_all(
         FLERR,
-        "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!");
+        fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!",
+                    style));
   }
 }
 
@@ -1612,7 +1632,8 @@ void FixPIMDLangevin::compute_p_cv()
   } else {
     error->universe_all(
         FLERR,
-        "Unknown method parameter for fix pimd/langevin. Only nmpimd and pimd are supported!");
+        fmt::format("Unknown method parameter for fix {}. Only nmpimd and pimd are supported!",
+                    style));
   }
 }
 

src/REPLICA/fix_pimd_langevin_bosonic.cpp

@@ -86,10 +86,12 @@ FixPIMDBLangevin::FixPIMDBLangevin(LAMMPS *lmp, int narg, char **arg) :
   }
 
   method = PIMD;
-
   size_vector = 6;
-
   memory->create(f_tag_order, nbosons, 3, "FixPIMDBLangevin:f_tag_order");
+
+  if (cmode != SINGLE_PROC)
+    error->universe_all(FLERR,
+                        fmt::format("Fix {} only supports a single processor per bead", style));
 }
 
 /* ---------------------------------------------------------------------- */
@@ -98,7 +100,7 @@ FixPIMDBLangevin::~FixPIMDBLangevin()
 {
   memory->destroy(f_tag_order);
   for (int i = 0; i < filtered_narg; ++i) delete[] filtered_args[i];
-  memory->destroy(filtered_args);
+  delete[] filtered_args;
   delete bosonic_exchange;
 }
 

src/REPLICA/fix_pimd_nvt.cpp

@@ -89,26 +89,28 @@ FixPIMDNVT::FixPIMDNVT(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
         method = CMD;
       else
         error->universe_all(
-            FLERR, fmt::format("Unknown method parameter {} for fix pimd/nvt", arg[i + 1]));
+            FLERR, fmt::format("Unknown method parameter {} for fix {}", arg[i + 1], style));
     } else if (strcmp(arg[i], "fmass") == 0) {
       fmass = utils::numeric(FLERR, arg[i + 1], false, lmp);
       if ((fmass < 0.0) || (fmass > np))
-        error->universe_all(FLERR, fmt::format("Invalid fmass value {} for fix pimd/nvt", fmass));
+        error->universe_all(FLERR, fmt::format("Invalid fmass value {} for fix {}", fmass, style));
     } else if (strcmp(arg[i], "sp") == 0) {
       sp = utils::numeric(FLERR, arg[i + 1], false, lmp);
-      if (sp < 0.0) error->universe_all(FLERR, "Invalid sp value for fix pimd/nvt");
+      if (sp < 0.0) error->universe_all(FLERR, fmt::format("Invalid sp value for fix {}", style));
     } else if (strcmp(arg[i], "temp") == 0) {
       nhc_temp = utils::numeric(FLERR, arg[i + 1], false, lmp);
-      if (nhc_temp < 0.0) error->universe_all(FLERR, "Invalid temp value for fix pimd/nvt");
+      if (nhc_temp < 0.0)
+        error->universe_all(FLERR, fmt::format("Invalid temp value for fix {}", style));
     } else if (strcmp(arg[i], "nhc") == 0) {
       nhc_nchain = utils::inumeric(FLERR, arg[i + 1], false, lmp);
-      if (nhc_nchain < 2) error->universe_all(FLERR, "Invalid nhc value for fix pimd/nvt");
+      if (nhc_nchain < 2)
+        error->universe_all(FLERR, fmt::format("Invalid nhc value for fix {}", style));
     } else
-      error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix pimd/nvt", arg[i]));
+      error->universe_all(FLERR, fmt::format("Unknown keyword {} for fix {}", arg[i], style));
   }
 
   if (strcmp(update->unit_style, "lj") == 0)
-    error->all(FLERR, "Fix pimd/nvt does not support lj units");
+    error->all(FLERR, fmt::format("Fix {} does not support lj units", style));
 
   /* Initiation */
 
@@ -187,10 +189,10 @@ int FixPIMDNVT::setmask()
 void FixPIMDNVT::init()
 {
   if (atom->map_style == Atom::MAP_NONE)
-    error->universe_all(FLERR, "Fix pimd/nvt requires an atom map, see atom_modify");
+    error->universe_all(FLERR, fmt::format("Fix {} requires an atom map, see atom_modify", style));
 
   if (universe->me == 0 && universe->uscreen)
-    fprintf(universe->uscreen, "Fix pimd/nvt initializing Path-Integral ...\n");
+    utils::print(universe->uscreen, "Fix {} initializing Path-Integral ...\n", style);
 
   // prepare the constants
 
@@ -539,13 +541,15 @@ void FixPIMDNVT::nmpimd_transform(double **src, double **des, double *vector)
 
 /* ---------------------------------------------------------------------- */
 
-void FixPIMDNVT::pre_spring_force_estimators(){
+void FixPIMDNVT::pre_spring_force_estimators()
+{
   vir_estimator();
 }
 
 /* ---------------------------------------------------------------------- */
 
-void FixPIMDNVT::vir_estimator() {
+void FixPIMDNVT::vir_estimator()
+{
   double **x = atom->x;
   double **f = atom->f;
   int nlocal = atom->nlocal;

src/REPLICA/fix_pimd_nvt_bosonic.cpp

@@ -26,6 +26,7 @@
 #include "bosonic_exchange.h"
 
 #include "atom.h"
+#include "comm.h"
 #include "error.h"
 #include "force.h"
 #include "universe.h"
@@ -46,6 +47,9 @@ FixPIMDBNVT::FixPIMDBNVT(LAMMPS *lmp, int narg, char **arg) : FixPIMDNVT(lmp, na
     error->universe_all(FLERR,
                         "Method not supported in fix pimdb/nvt; only methods PIMD and NMPIMD");
   }
+  if (comm->nprocs != 1)
+    error->universe_all(FLERR,
+                        fmt::format("Fix {} only supports a single processor per bead", style));
 }
 
 /* ---------------------------------------------------------------------- */

src/SPIN/compute_spin.cpp

@@ -105,6 +105,7 @@ void ComputeSpin::init()
   // init length of vector of ptrs to Pair/Spin styles
 
   if (npairspin > 0) {
+    delete[] spin_pairs;
     spin_pairs = new PairSpin*[npairspin];
   }
 
@@ -142,6 +143,7 @@ void ComputeSpin::init()
   nprecspin = precfixes.size();
 
   if (nprecspin > 0) {
+    delete[] lockprecessionspin;
     lockprecessionspin = new FixPrecessionSpin *[nprecspin];
     precession_spin_flag = 1;
 

src/SPIN/fix_nve_spin.cpp

@@ -185,6 +185,7 @@ void FixNVESpin::init()
   // init length of vector of ptrs to Pair/Spin styles
 
   if (npairspin > 0) {
+    delete[] spin_pairs;
     spin_pairs = new PairSpin*[npairspin];
   }
 
@@ -231,6 +232,7 @@ void FixNVESpin::init()
   // init length of vector of ptrs to precession/spin styles
 
   if (nprecspin > 0) {
+    delete[] lockprecessionspin;
     lockprecessionspin = new FixPrecessionSpin*[nprecspin];
   }
 
@@ -582,7 +584,8 @@ void FixNVESpin::sectoring()
   }
 
   if (rv == 0.0)
-   error->all(FLERR,"Illegal sectoring operation");
+   error->all(FLERR, Error::NOLASTLINE,
+              "No suitable cutoff found for sectoring operation: rv = {}", rv);
 
   double rax = rsx/rv;
   double ray = rsy/rv;
@@ -598,7 +601,8 @@ void FixNVESpin::sectoring()
   nsectors = sec[0]*sec[1]*sec[2];
 
   if (sector_flag && (nsectors != 8))
-    error->all(FLERR,"Illegal sectoring operation");
+    error->all(FLERR, Error::NOLASTLINE,
+               "Illegal sectoring operation resulting in {} sectors instead of 8", nsectors);
 
   rsec[0] = rsx;
   rsec[1] = rsy;

src/STUBS/mpi.cpp

@@ -300,6 +300,14 @@ int MPI_Irecv(void *buf, int count, MPI_Datatype datatype, int source, int tag,
 
 /* ---------------------------------------------------------------------- */
 
+int MPI_Iprobe(int, int, MPI_Comm, int *flag, MPI_Status *)
+{
+  if (flag) *flag = 0;
+  return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
 int MPI_Wait(MPI_Request *request, MPI_Status *status)
 {
   static int callcount = 0;