Merge pull request #4614 from akohlmey/collected-small-fixes
Collected small changes and fixes
This commit is contained in:
Axel Kohlmeyer
@ -113,7 +113,6 @@ OPT.
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* :doc:`mvv/tdpd <fix_mvv_dpd>`
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* :doc:`mvv/tdpd <fix_mvv_dpd>`
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* :doc:`neb <fix_neb>`
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* :doc:`neb <fix_neb>`
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* :doc:`neb/spin <fix_neb_spin>`
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* :doc:`neb/spin <fix_neb_spin>`
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* :doc:`neighbor/swap <fix_neighbor_swap>`
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* :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
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* :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
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* :doc:`nph (ko) <fix_nh>`
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* :doc:`nph (ko) <fix_nh>`
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* :doc:`nph/asphere (o) <fix_nph_asphere>`
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* :doc:`nph/asphere (o) <fix_nph_asphere>`
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@ -21,8 +21,8 @@ You can follow the LAMMPS development on 4 different git branches:
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* **develop** : this branch follows the ongoing development and is
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* **develop** : this branch follows the ongoing development and is
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updated with every merge commit of a pull request
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updated with every merge commit of a pull request
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* **release** : this branch is updated with every "feature release";
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* **release** : this branch is updated with every "feature release"
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updates are always "fast-forward" merges from *develop*
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and updates are always "fast-forward" merges from *develop*
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* **maintenance** : this branch collects back-ported bug fixes from the
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* **maintenance** : this branch collects back-ported bug fixes from the
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*develop* branch to the *stable* branch. It is used to update the
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*develop* branch to the *stable* branch. It is used to update the
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*stable* branch for "stable update releases".
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*stable* branch for "stable update releases".
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@ -292,7 +292,6 @@ accelerated styles exist.
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* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
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* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
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* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
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* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
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* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
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* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
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* :doc:`neighbor/swap <fix_neighbor_swap>` - kinetic Monte Carlo (kMC) atom swapping
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* :doc:`nonaffine/displacement <fix_nonaffine_displacement>` - calculate nonaffine displacement of atoms
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* :doc:`nonaffine/displacement <fix_nonaffine_displacement>` - calculate nonaffine displacement of atoms
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* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
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* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
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* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
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* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
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@ -1,264 +0,0 @@
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.. index:: fix neighbor/swap
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fix neighbor/swap command
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=========================
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Syntax
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""""""
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.. code-block:: LAMMPS
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fix ID group-ID neighbor/swap N X seed T R0 voro-ID keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* neighbor/swap = style name of this fix command
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* N = invoke this fix every N steps
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* X = number of swaps to attempt every N steps
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* seed = random # seed (positive integer)
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* T = scaling temperature of the MC swaps (temperature units)
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* R0 = scaling swap probability of the MC swaps (distance units)
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* voro-ID = valid voronoi compute id (compute voronoi/atom)
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* one or more keyword/value pairs may be appended to args
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* keywords *types* and *diff* are mutually exclusive, but one must be specified
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* keyword = *types* or *diff* or *ke* or *region* or *rates*
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.. parsed-literal::
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*types* values = two or more atom types (Integers in range [1,Ntypes] or type labels)
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*diff* values = one atom type
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*ke* value = *yes* or *no*
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*yes* = kinetic energy is conserved after atom swaps
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*no* = no conservation of kinetic energy after atom swaps
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*region* value = region-ID
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region-ID = ID of region to use as an exchange/move volume
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*rates* values = V1 V2 . . . Vntypes values to conduct variable diffusion for different atom types (unitless)
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute voroN all voronoi/atom neighbors yes
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fix mc all neighbor/swap 10 160 15238 1000.0 3.0 voroN diff 2
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fix myFix all neighbor/swap 100 1 12345 298.0 3.0 voroN region my_swap_region types 5 6
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fix kmc all neighbor/swap 1 100 345 1.0 3.0 voroN diff 3 rates 3 1 6
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Description
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"""""""""""
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.. versionadded:: TBD
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This fix performs Monte-Carlo (MC) evaluations to enable kinetic
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Monte Carlo (kMC)-type behavior during MD simulation by allowing
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neighboring atoms to swap their positions. In contrast to the :doc:`fix
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atom/swap <fix_atom_swap>` command which swaps pairs of atoms anywhere
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in the simulation domain, the restriction of the MC swapping to
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neighbors enables a hybrid MD/kMC-like simulation.
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Neighboring atoms are defined by using a Voronoi tesselation performed
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by the :doc:`compute voronoi/atom <compute_voronoi_atom>` command.
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Two atoms are neighbors if their Voronoi cells share a common face
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(3d) or edge (2d).
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The selection of a swap neighbor is made using a distance-based
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criterion for weighting the selection probability of each swap, in the
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same manner as kMC selects a next event using relative probabilities.
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The acceptance or rejection of each swap is determined via the
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Metropolis criterion after evaluating the change in system energy due
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to the swap.
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A detailed explanation of the original implementation of this
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algorithm can be found in :ref:`(Tavenner 2023) <TavennerMDkMC>`
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where it was used to simulated accelerated diffusion in an MD context.
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Simulating inherently kinetically-limited behaviors which rely on rare
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events (such as atomic diffusion in a solid) is challenging for
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traditional MD since its relatively short timescale will not naturally
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sample many events. This fix addresses this challenge by allowing rare
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neighbor hopping events to be sampled in a kMC-like fashion at a much
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faster rate (set by the specified *N* and *X* parameters). This enables
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the processes of atomic diffusion to be approximated during an MD
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simulation, effectively decoupling the MD atomic vibrational timescale
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and the atomic hopping (kMC event) timescale.
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The algorithm implemented by this fix is as follows:
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- The MD simulation is paused every *N* steps
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- A Voronoi tesselation is performed for the current atom configuration.
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- Then *X* atom swaps are attempted, one after the other.
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- For each swap, an atom *I* is selected randomly from the list of
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atom types specified by either the *types* or *diff* keywords.
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- One of *I*'s Voronoi neighbors *J* is selected using the
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distance-weighted probability for each neighbor detailed below.
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- The *I,J* atom IDs are communicated to all processors so that a
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global energy evaluation can be performed for the post-swap state
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of the system.
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- The swap is accepted or rejected based on the Metropolis criterion
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using the energy change of the system and the specified temperature
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*T*.
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Here are a few comments on the computational cost of the swapping
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algorithm.
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1. The cost of a global energy evaluation is similar to that of an MD
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timestep.
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2. Similar to other MC algorithms in LAMMPS, improved parallel
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efficiency is achieved with a smaller number of atoms per
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processor than would typically be used in an standard MD
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simulation. This is because the per-energy evaluation cost
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increases relative to the balance of MD/MC steps as indicated by
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1., but the communication cost remains relatively constant for a
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given number of MD steps.
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3. The MC portion of the simulation will run dramatically slower if
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the pair style uses different cutoffs for different atom types (or
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type pairs). This is because each atom swap then requires a
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rebuild of the neighbor list to ensure the post-swap global energy
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can be computed correctly.
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Limitations are imposed on selection of *I,J* atom pairs to avoid
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swapping of atoms which are outside of a reasonable cutoff (e.g. due to
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a Voronoi tesselation near free surfaces) though the use of a
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distance-weighted probability scaling.
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----------
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This section gives more details on other arguments and keywords.
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The random number generator (RNG) used by all the processors for MC
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operations is initialized with the specified *seed*.
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The distance-based probability is weighted by the specified *R0* which
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sets the radius :math:`r_0` in this formula
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.. math::
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p_{ij} = e^{(\frac{r_{ij}}{r_0})^2}
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where :math:`p_{ij}` is the probability of selecting atom :math:`j` to
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swap with atom :math:`i`. Typically, a value for *R0* around the
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average nearest-neighbor spacing is appropriate. Since this is simply a
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probability weighting, the swapping behavior is not very sensitive to
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the exact value of *R0*.
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The required *voro-ID* value is the compute-ID of a
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:doc:`compute voronoi/atom <compute_voronoi_atom>` command like
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this:
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.. code-block:: LAMMPS
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compute compute-ID group-ID voronoi/atom neighbors yes
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It must return per-atom list of valid neighbor IDs as in the
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:doc:`compute voronoi/atom <compute_voronoi_atom>` command.
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The keyword *types* takes two or more atom types as its values. Only
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atoms *I* of the first atom type will be selected. Only atoms *J* of the
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remaining atom types will be considered as potential swap partners.
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The keyword *diff* take a single atom type as its value. Only atoms
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*I* of the that atom type will be selected. Atoms *J* of all
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remaining atom types will be considered as potential swap partners.
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This includes the atom type specified with the *diff* keyword to
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account for self-diffusive hops between two atoms of the same type.
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Note that the *neighbors yes* option must be enabled for use with this
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fix. The group-ID should include all the atoms which this fix will
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potentially select. I.e. the group-ID used in the voronoi compute should
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include the same atoms as that indicated by the *types* keyword. If the
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*diff* keyword is used, the group-ID should include atoms of all types
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in the simulation.
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The keyword *ke* takes *yes* (default) or *no* as its value. It two
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atoms are swapped with different masses, then a value of *yes* will
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rescale their respective velocities to conserve the kinetic energy of
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the system. A value of *no* will perform no rescaling, so that
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kinetic energy is not conserved. See the restriction on this keyword
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below.
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The *region* keyword takes a *region-ID* as its value. If specified,
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then only atoms *I* and *J* within the geometric region will be
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considered as swap partners. See the :doc:`region <region>` command
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for details. This means the group-ID for the :doc:`compute
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voronoi/atom <compute_voronoi_atom>` command also need only contain
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atoms within the region.
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The keyword *rates* can modify the swap rate based on the type of atom
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*J*. Ntype values must be specified, where Ntype = the number of atom
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types in the system. Each value is used to scale the probability
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weighting given by the equation above. In the third example command
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above, a simulation has 3 atoms types. Atom *I*s of type 1 are
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eligible for swapping. Swaps may occur with atom *J*s of all 3 types.
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Assuming all *J* atoms are equidistant from an atom *I*, *J* atoms of
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type 1 will be 3x more likely to be selected as a swap partner than
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atoms of type 2. And *J* atoms of type 3 will be 6.5x more likely to
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be selected than atoms of type 2. If the *rates* keyword is not used,
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all atom types will be treated with the same probability during selection
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of swap attempts.
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This fix writes the state of the fix to :doc:`binary restart files
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<restart>`. This includes information about the random number generator
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seed, the next timestep for MC exchanges, and the number of exchange
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attempts and successes. See the :doc:`read_restart <read_restart>`
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command for info on how to re-specify a fix in an input script that
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reads a restart file, so that the operation of the fix continues in an
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uninterrupted fashion.
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None of the :doc:`fix_modify <fix_modify>` options are relevant to this
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fix.
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This fix computes a global vector of length 2, which can be accessed
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by various :doc:`output commands <Howto_output>`. The vector values are
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the following global cumulative quantities:
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#. swap attempts
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#. swap accepts
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The vector values calculated by this fix are "intensive".
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during
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:doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix is part of the MC package. It is only enabled if LAMMPS was
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built with that package. See the :doc:`Build package <Build_package>`
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doc page for more info. Also this fix requires that the :ref:`VORONOI
|
|
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package <PKG-VORONOI>` is installed, otherwise the fix will not be
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compiled.
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|
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|
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The :doc:`compute voronoi/atom <compute_voronoi_atom>` command
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|
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referenced by the required voro-ID must return neighboring atoms as
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|
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illustrated in the examples above.
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If this fix is used with systems that do not have per-type masses
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|
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(e.g. atom style sphere), the *ke* keyword must be set to *off* since
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the implemented algorithm will not be able to re-scale velocities
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|
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properly.
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|
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Related commands
|
|
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""""""""""""""""
|
|
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|
|
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:doc:`fix nvt <fix_nh>`, :doc:`compute voronoi/atom <compute_voronoi_atom>`
|
|
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:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`,
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|
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:doc:`fix atom/swap <fix_atom_swap>`, :doc:`fix mol/swap <fix_mol_swap>`,
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|
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:doc:`fix sgcmc <fix_sgcmc>`
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|
||||||
|
|
||||||
Default
|
|
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"""""""
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|
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The option defaults are *ke* = yes and *rates* = 1 for all atom types.
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----------
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|
|
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.. _TavennerMDkMC:
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|
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|
|
||||||
**(Tavenner 2023)** J Tavenner, M Mendelev, J Lawson, Computational
|
|
||||||
Materials Science, 218, 111929 (2023).
|
|
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@ -370,6 +370,17 @@ latex_elements = {
|
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{%
|
{%
|
||||||
\hypersetup{pageanchor=false}% avoid duplicate destination warnings
|
\hypersetup{pageanchor=false}% avoid duplicate destination warnings
|
||||||
\begin{titlepage}%
|
\begin{titlepage}%
|
||||||
|
\sffamily\Large
|
||||||
|
The LAMMPS developers are thinking about dropping the PDF format version of
|
||||||
|
the LAMMPS manual. This would allow us to focus on the HTML version, use
|
||||||
|
HTML-only features, and skip checking if the documentation source files,
|
||||||
|
especially the embedded mathematical expressions, are compatible with \LaTeX{} output.
|
||||||
|
|
||||||
|
Please let us know how you feel about this change by sending an email to
|
||||||
|
\texttt{developers@lammps.org} stating whether you agree or disagree with
|
||||||
|
removing support for the PDF format version of the manual and optionally
|
||||||
|
provide arguments for your preference.
|
||||||
|
\clearpage
|
||||||
\sffamily\bfseries
|
\sffamily\bfseries
|
||||||
\begingroup % for PDF information dictionary
|
\begingroup % for PDF information dictionary
|
||||||
\def\endgraf{ }\def\and{\& }%
|
\def\endgraf{ }\def\and{\& }%
|
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|
|||||||
@ -1 +0,0 @@
|
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../../../potentials/MoCoNiVFeAlCr_2nn.meam
|
|
||||||
@ -1,46 +0,0 @@
|
|||||||
# May 2025
|
|
||||||
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
|
|
||||||
# Created by Jacob Tavenner, Baylor University
|
|
||||||
|
|
||||||
# Initiation -------------------------------------
|
|
||||||
units metal
|
|
||||||
dimension 3
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|
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boundary p p p
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atom_style atomic
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||||||
|
|
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# Atom Definition --------------------------------
|
|
||||||
lattice fcc 3.762
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|
||||||
region whole block 0 1 0 1 0 1
|
|
||||||
create_box 2 whole
|
|
||||||
create_atoms 1 region whole
|
|
||||||
|
|
||||||
replicate 6 16 6
|
|
||||||
|
|
||||||
region puck block INF INF 7 9 INF INF
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|
||||||
set region puck type 2
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|
||||||
|
|
||||||
# Force Fields -----------------------------------
|
|
||||||
pair_style meam
|
|
||||||
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
|
|
||||||
|
|
||||||
# Settings ---------------------------------------
|
|
||||||
timestep 0.002
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
# Computations -----------------------------------
|
|
||||||
compute voroN all voronoi/atom neighbors yes
|
|
||||||
|
|
||||||
run 0
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
|
|
||||||
|
|
||||||
# Execution --------------------------------------
|
|
||||||
|
|
||||||
velocity all create 2400 908124 loop geom
|
|
||||||
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
|
|
||||||
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
|
|
||||||
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
|
|
||||||
|
|
||||||
run 1000
|
|
||||||
|
|
||||||
#write_data pulse_center.data
|
|
||||||
@ -1,47 +0,0 @@
|
|||||||
# May 2025
|
|
||||||
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
|
|
||||||
# Created by Jacob Tavenner, Baylor University
|
|
||||||
|
|
||||||
# Initiation -------------------------------------
|
|
||||||
units metal
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
|
|
||||||
# Atom Definition --------------------------------
|
|
||||||
lattice fcc 3.762
|
|
||||||
region whole block 0 1 0 1 0 1
|
|
||||||
create_box 2 whole
|
|
||||||
create_atoms 1 region whole
|
|
||||||
|
|
||||||
replicate 6 16 6
|
|
||||||
|
|
||||||
region puck block INF INF INF 2 INF INF
|
|
||||||
set region puck type 2
|
|
||||||
|
|
||||||
# Force Fields -----------------------------------
|
|
||||||
pair_style meam
|
|
||||||
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
|
|
||||||
|
|
||||||
# Settings ---------------------------------------
|
|
||||||
timestep 0.002
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
# Computations -----------------------------------
|
|
||||||
compute voroN all voronoi/atom neighbors yes
|
|
||||||
|
|
||||||
run 0
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
|
|
||||||
|
|
||||||
# Execution --------------------------------------
|
|
||||||
|
|
||||||
velocity all create 2400 908124 loop geom
|
|
||||||
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
|
|
||||||
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
|
|
||||||
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
|
|
||||||
|
|
||||||
run 1000
|
|
||||||
|
|
||||||
#write_data pulse_end.data
|
|
||||||
@ -1 +0,0 @@
|
|||||||
../../../potentials/library_2nn.meam
|
|
||||||
@ -1,154 +0,0 @@
|
|||||||
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# May 2025
|
|
||||||
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
|
|
||||||
# Created by Jacob Tavenner, Baylor University
|
|
||||||
|
|
||||||
# Initiation -------------------------------------
|
|
||||||
units metal
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
# Atom Definition --------------------------------
|
|
||||||
lattice fcc 3.762
|
|
||||||
Lattice spacing in x,y,z = 3.762 3.762 3.762
|
|
||||||
region whole block 0 1 0 1 0 1
|
|
||||||
create_box 2 whole
|
|
||||||
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
create_atoms 1 region whole
|
|
||||||
Created 4 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
|
|
||||||
replicate 6 16 6
|
|
||||||
Replication is creating a 6x16x6 = 576 times larger system...
|
|
||||||
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
2304 atoms
|
|
||||||
replicate CPU = 0.000 seconds
|
|
||||||
|
|
||||||
region puck block INF INF 7 9 INF INF
|
|
||||||
set region puck type 2
|
|
||||||
Setting atom values ...
|
|
||||||
360 settings made for type
|
|
||||||
|
|
||||||
# Force Fields -----------------------------------
|
|
||||||
pair_style meam
|
|
||||||
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
|
|
||||||
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
|
|
||||||
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
|
|
||||||
|
|
||||||
# Settings ---------------------------------------
|
|
||||||
timestep 0.002
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
# Computations -----------------------------------
|
|
||||||
compute voroN all voronoi/atom neighbors yes
|
|
||||||
|
|
||||||
run 0
|
|
||||||
WARNING: No fixes with time integration, atoms won't move
|
|
||||||
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
|
|
||||||
Neighbor list info ...
|
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 6.8
|
|
||||||
ghost atom cutoff = 6.8
|
|
||||||
binsize = 3.4, bins = 7 18 7
|
|
||||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
||||||
(1) pair meam, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
(2) pair meam, perpetual, half/full from (1)
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: halffull/newton
|
|
||||||
stencil: none
|
|
||||||
bin: none
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -9674.3728 0 -9674.3728 -212400.94
|
|
||||||
Loop time of 1.202e-06 on 1 procs for 0 steps with 2304 atoms
|
|
||||||
|
|
||||||
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 | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Other | | 1.202e-06 | | |100.00
|
|
||||||
|
|
||||||
Nlocal: 2304 ave 2304 max 2304 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 4735 ave 4735 max 4735 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 99072 ave 99072 max 99072 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 198144 ave 198144 max 198144 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 198144
|
|
||||||
Ave neighs/atom = 86
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
|
|
||||||
|
|
||||||
# Execution --------------------------------------
|
|
||||||
|
|
||||||
velocity all create 2400 908124
|
|
||||||
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
|
|
||||||
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
|
|
||||||
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
|
|
||||||
|
|
||||||
run 1000
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
|
|
||||||
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
|
|
||||||
0 2400 -187517.52 -187403.07 -187750.14 -187399.35 22.572 60.192 22.572 30667.534 -9674.3728 0 0
|
|
||||||
100 1664.9956 14000 14280.682 15095.077 12624.241 21.635315 57.726568 21.64791 27036.778 -9592.8978 24 22
|
|
||||||
200 1560.0093 -5452.2434 -5749.5816 -2957.4228 -7649.7258 21.734212 58.085959 21.724853 27426.596 -9562.8822 48 45
|
|
||||||
300 1586.4553 2030.9253 2776.4677 775.50538 2540.803 21.678654 58.101753 21.654423 27275.215 -9571.1308 72 66
|
|
||||||
400 1603.6896 -223.16773 156.17673 -478.47929 -347.20061 21.701021 58.098904 21.657752 27306.213 -9576.4456 96 90
|
|
||||||
500 1618.236 -925.51874 -1640.9078 451.6228 -1587.2713 21.718334 58.042685 21.666081 27312.054 -9581.2045 120 110
|
|
||||||
600 1581.9995 290.10126 1359.1314 1407.5434 -1896.371 21.679813 58.086147 21.692118 27316.815 -9570.4803 144 132
|
|
||||||
700 1568.3261 1387.3472 938.81523 2159.3686 1063.8577 21.685928 58.075626 21.67273 27295.153 -9566.2914 168 155
|
|
||||||
800 1607.1531 46.792964 -453.90265 -1533.3908 2127.6723 21.685188 58.202356 21.628338 27297.753 -9577.7848 192 177
|
|
||||||
900 1573.4747 -84.225488 548.90935 -1356.7479 555.16208 21.69634 58.150052 21.651847 27316.908 -9567.7039 216 196
|
|
||||||
1000 1609.2136 1215.0833 764.08936 3301.0811 -419.92053 21.683731 58.000401 21.68726 27275.31 -9578.2843 240 219
|
|
||||||
Loop time of 31.6263 on 1 procs for 1000 steps with 2304 atoms
|
|
||||||
|
|
||||||
Performance: 5.464 ns/day, 4.393 hours/ns, 31.619 timesteps/s, 72.851 katom-step/s
|
|
||||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 28.487 | 28.487 | 28.487 | 0.0 | 90.07
|
|
||||||
Neigh | 0.22789 | 0.22789 | 0.22789 | 0.0 | 0.72
|
|
||||||
Comm | 0.010808 | 0.010808 | 0.010808 | 0.0 | 0.03
|
|
||||||
Output | 0.00033526 | 0.00033526 | 0.00033526 | 0.0 | 0.00
|
|
||||||
Modify | 2.8963 | 2.8963 | 2.8963 | 0.0 | 9.16
|
|
||||||
Other | | 0.003905 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 2304 ave 2304 max 2304 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 4750 ave 4750 max 4750 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 130023 ave 130023 max 130023 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 260046 ave 260046 max 260046 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 260046
|
|
||||||
Ave neighs/atom = 112.86719
|
|
||||||
Neighbor list builds = 65
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
#write_data pulse_center.data
|
|
||||||
Total wall time: 0:00:31
|
|
||||||
@ -1,154 +0,0 @@
|
|||||||
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# May 2025
|
|
||||||
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
|
|
||||||
# Created by Jacob Tavenner, Baylor University
|
|
||||||
|
|
||||||
# Initiation -------------------------------------
|
|
||||||
units metal
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
# Atom Definition --------------------------------
|
|
||||||
lattice fcc 3.762
|
|
||||||
Lattice spacing in x,y,z = 3.762 3.762 3.762
|
|
||||||
region whole block 0 1 0 1 0 1
|
|
||||||
create_box 2 whole
|
|
||||||
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
create_atoms 1 region whole
|
|
||||||
Created 4 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
|
|
||||||
replicate 6 16 6
|
|
||||||
Replication is creating a 6x16x6 = 576 times larger system...
|
|
||||||
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
|
|
||||||
1 by 4 by 1 MPI processor grid
|
|
||||||
2304 atoms
|
|
||||||
replicate CPU = 0.000 seconds
|
|
||||||
|
|
||||||
region puck block INF INF 7 9 INF INF
|
|
||||||
set region puck type 2
|
|
||||||
Setting atom values ...
|
|
||||||
360 settings made for type
|
|
||||||
|
|
||||||
# Force Fields -----------------------------------
|
|
||||||
pair_style meam
|
|
||||||
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
|
|
||||||
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
|
|
||||||
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
|
|
||||||
|
|
||||||
# Settings ---------------------------------------
|
|
||||||
timestep 0.002
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
# Computations -----------------------------------
|
|
||||||
compute voroN all voronoi/atom neighbors yes
|
|
||||||
|
|
||||||
run 0
|
|
||||||
WARNING: No fixes with time integration, atoms won't move
|
|
||||||
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
|
|
||||||
Neighbor list info ...
|
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 6.8
|
|
||||||
ghost atom cutoff = 6.8
|
|
||||||
binsize = 3.4, bins = 7 18 7
|
|
||||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
||||||
(1) pair meam, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
(2) pair meam, perpetual, half/full from (1)
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: halffull/newton
|
|
||||||
stencil: none
|
|
||||||
bin: none
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -9674.3728 0 -9674.3728 -212400.94
|
|
||||||
Loop time of 1.422e-06 on 4 procs for 0 steps with 2304 atoms
|
|
||||||
|
|
||||||
35.2% 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 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Other | | 1.422e-06 | | |100.00
|
|
||||||
|
|
||||||
Nlocal: 576 ave 576 max 576 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 2131 ave 2131 max 2131 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 24768 ave 24768 max 24768 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 49536 ave 49536 max 49536 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 198144
|
|
||||||
Ave neighs/atom = 86
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
|
|
||||||
|
|
||||||
# Execution --------------------------------------
|
|
||||||
|
|
||||||
velocity all create 2400 908124
|
|
||||||
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
|
|
||||||
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
|
|
||||||
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
|
|
||||||
|
|
||||||
run 1000
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
|
|
||||||
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
|
|
||||||
0 2400 -187517.52 -187403.09 -187750.05 -187399.42 22.572 60.192 22.572 30667.534 -9674.3728 0 0
|
|
||||||
100 1668.8754 13300.763 12419.304 15568.772 11914.212 21.636248 57.724775 21.647685 27036.823 -9594.7526 24 23
|
|
||||||
200 1584.9699 -5686.0414 -4741.8496 -5914.7681 -6401.5064 21.729384 58.060532 21.730736 27415.923 -9571.0639 48 46
|
|
||||||
300 1582.0473 2806.2983 3413.4122 2716.0124 2289.4702 21.6679 58.033587 21.694744 27280.402 -9570.5549 72 69
|
|
||||||
400 1582.5825 845.29268 -849.61221 2123.5339 1261.9563 21.676298 58.14253 21.656418 27293.905 -9570.7948 96 93
|
|
||||||
500 1591.7285 -501.17955 1151.9743 -1719.3712 -936.14174 21.696367 58.157211 21.648308 27315.839 -9573.5089 120 116
|
|
||||||
600 1610.708 -821.74669 -1002.4957 291.88502 -1754.6294 21.730338 58.008213 21.661226 27304.8 -9579.5573 144 138
|
|
||||||
700 1598.5176 -590.00633 -1844.42 408.97706 -334.57602 21.712908 57.96131 21.698129 27307.281 -9575.8973 168 162
|
|
||||||
800 1584.3478 330.16711 666.88818 74.698331 248.91482 21.650908 58.045055 21.719838 27295.933 -9571.9268 192 186
|
|
||||||
900 1557.9946 1471.1207 2124.6512 1526.9937 761.71731 21.645578 58.156083 21.681637 27293.323 -9564.4385 216 207
|
|
||||||
1000 1582.5312 379.57005 -602.96446 2696.737 -955.06238 21.655418 58.231248 21.649581 27300.598 -9571.9879 240 227
|
|
||||||
Loop time of 9.1632 on 4 procs for 1000 steps with 2304 atoms
|
|
||||||
|
|
||||||
Performance: 18.858 ns/day, 1.273 hours/ns, 109.132 timesteps/s, 251.440 katom-step/s
|
|
||||||
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 7.867 | 7.9923 | 8.1311 | 4.3 | 87.22
|
|
||||||
Neigh | 0.054997 | 0.057518 | 0.060145 | 1.0 | 0.63
|
|
||||||
Comm | 0.017529 | 0.14801 | 0.27408 | 29.5 | 1.62
|
|
||||||
Output | 0.00015963 | 0.00017216 | 0.00020869 | 0.0 | 0.00
|
|
||||||
Modify | 0.95227 | 0.96325 | 0.9917 | 1.7 | 10.51
|
|
||||||
Other | | 0.001983 | | | 0.02
|
|
||||||
|
|
||||||
Nlocal: 576 ave 609 max 540 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
Nghost: 2161.5 ave 2173 max 2151 min
|
|
||||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
|
||||||
Neighs: 32450.2 ave 35422 max 29271 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
FullNghs: 64900.5 ave 70800 max 58684 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
|
|
||||||
Total # of neighbors = 259602
|
|
||||||
Ave neighs/atom = 112.67448
|
|
||||||
Neighbor list builds = 62
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
#write_data pulse_center.data
|
|
||||||
Total wall time: 0:00:09
|
|
||||||
@ -1,155 +0,0 @@
|
|||||||
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# May 2025
|
|
||||||
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
|
|
||||||
# Created by Jacob Tavenner, Baylor University
|
|
||||||
|
|
||||||
# Initiation -------------------------------------
|
|
||||||
units metal
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
|
|
||||||
# Atom Definition --------------------------------
|
|
||||||
lattice fcc 3.762
|
|
||||||
Lattice spacing in x,y,z = 3.762 3.762 3.762
|
|
||||||
region whole block 0 1 0 1 0 1
|
|
||||||
create_box 2 whole
|
|
||||||
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
create_atoms 1 region whole
|
|
||||||
Created 4 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
|
|
||||||
replicate 6 16 6
|
|
||||||
Replication is creating a 6x16x6 = 576 times larger system...
|
|
||||||
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
2304 atoms
|
|
||||||
replicate CPU = 0.000 seconds
|
|
||||||
|
|
||||||
region puck block INF INF INF 2 INF INF
|
|
||||||
set region puck type 2
|
|
||||||
Setting atom values ...
|
|
||||||
360 settings made for type
|
|
||||||
|
|
||||||
# Force Fields -----------------------------------
|
|
||||||
pair_style meam
|
|
||||||
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
|
|
||||||
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
|
|
||||||
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
|
|
||||||
|
|
||||||
# Settings ---------------------------------------
|
|
||||||
timestep 0.002
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
# Computations -----------------------------------
|
|
||||||
compute voroN all voronoi/atom neighbors yes
|
|
||||||
|
|
||||||
run 0
|
|
||||||
WARNING: No fixes with time integration, atoms won't move
|
|
||||||
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
|
|
||||||
Neighbor list info ...
|
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 6.8
|
|
||||||
ghost atom cutoff = 6.8
|
|
||||||
binsize = 3.4, bins = 7 18 7
|
|
||||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
||||||
(1) pair meam, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
(2) pair meam, perpetual, half/full from (1)
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: halffull/newton
|
|
||||||
stencil: none
|
|
||||||
bin: none
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -9674.3728 0 -9674.3728 -212400.94
|
|
||||||
Loop time of 1.232e-06 on 1 procs for 0 steps with 2304 atoms
|
|
||||||
|
|
||||||
81.2% 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 | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Other | | 1.232e-06 | | |100.00
|
|
||||||
|
|
||||||
Nlocal: 2304 ave 2304 max 2304 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 4735 ave 4735 max 4735 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 99072 ave 99072 max 99072 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 198144 ave 198144 max 198144 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 198144
|
|
||||||
Ave neighs/atom = 86
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
|
|
||||||
|
|
||||||
# Execution --------------------------------------
|
|
||||||
|
|
||||||
velocity all create 2400 908124 loop geom
|
|
||||||
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
|
|
||||||
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
|
|
||||||
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
|
|
||||||
|
|
||||||
run 1000
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
|
|
||||||
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
|
|
||||||
0 2400 -187517.52 -187464.47 -188202.62 -186885.48 22.572 60.192 22.572 30667.534 -9674.3728 0 0
|
|
||||||
100 1665.6154 14281.316 14426.547 14555.867 13861.534 21.637238 57.719793 21.637281 27022.733 -9594.4303 24 24
|
|
||||||
200 1603.3309 -7325.7341 -8878.1524 -5333.0485 -7766.0015 21.710246 58.122827 21.725933 27415.106 -9577.4545 48 48
|
|
||||||
300 1603.2974 207.19165 1983.4565 -1841.9518 480.07024 21.678227 58.079126 21.674033 27288.745 -9577.6391 72 69
|
|
||||||
400 1600.1515 810.95054 1087.969 802.04946 542.83316 21.683731 58.045848 21.678505 27285.662 -9576.6508 96 92
|
|
||||||
500 1629.8313 -2808.1005 -3197.9357 310.89931 -5537.265 21.683924 58.090375 21.697076 27330.229 -9585.5435 120 113
|
|
||||||
600 1598.8232 -67.845623 -1573.0718 -1526.7607 2896.2957 21.70213 58.12191 21.653853 27313.504 -9576.4147 144 137
|
|
||||||
700 1607.2185 154.66718 -1777.2469 2566.4705 -325.22208 21.712408 57.971553 21.678708 27287.033 -9579.1772 168 158
|
|
||||||
800 1582.559 -891.23631 -632.46037 -636.88203 -1404.3665 21.671936 58.127004 21.678224 27308.594 -9571.6663 192 180
|
|
||||||
900 1586.7172 -617.17083 -2495.5378 -2302.8766 2946.9018 21.658489 58.181921 21.668968 27305.771 -9572.9641 216 204
|
|
||||||
1000 1607.563 -389.8113 810.4908 298.84287 -2278.7676 21.624573 58.076745 21.724272 27283.183 -9579.5034 240 227
|
|
||||||
Loop time of 31.7733 on 1 procs for 1000 steps with 2304 atoms
|
|
||||||
|
|
||||||
Performance: 5.439 ns/day, 4.413 hours/ns, 31.473 timesteps/s, 72.514 katom-step/s
|
|
||||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 28.604 | 28.604 | 28.604 | 0.0 | 90.02
|
|
||||||
Neigh | 0.21293 | 0.21293 | 0.21293 | 0.0 | 0.67
|
|
||||||
Comm | 0.010645 | 0.010645 | 0.010645 | 0.0 | 0.03
|
|
||||||
Output | 0.00033194 | 0.00033194 | 0.00033194 | 0.0 | 0.00
|
|
||||||
Modify | 2.9411 | 2.9411 | 2.9411 | 0.0 | 9.26
|
|
||||||
Other | | 0.00448 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 2304 ave 2304 max 2304 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 4748 ave 4748 max 4748 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 130301 ave 130301 max 130301 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 260602 ave 260602 max 260602 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 260602
|
|
||||||
Ave neighs/atom = 113.10851
|
|
||||||
Neighbor list builds = 62
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
#write_data pulse_end.data
|
|
||||||
Total wall time: 0:00:31
|
|
||||||
@ -1,155 +0,0 @@
|
|||||||
LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# May 2025
|
|
||||||
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
|
|
||||||
# Created by Jacob Tavenner, Baylor University
|
|
||||||
|
|
||||||
# Initiation -------------------------------------
|
|
||||||
units metal
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
|
|
||||||
# Atom Definition --------------------------------
|
|
||||||
lattice fcc 3.762
|
|
||||||
Lattice spacing in x,y,z = 3.762 3.762 3.762
|
|
||||||
region whole block 0 1 0 1 0 1
|
|
||||||
create_box 2 whole
|
|
||||||
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
create_atoms 1 region whole
|
|
||||||
Created 4 atoms
|
|
||||||
using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
|
|
||||||
create_atoms CPU = 0.000 seconds
|
|
||||||
|
|
||||||
replicate 6 16 6
|
|
||||||
Replication is creating a 6x16x6 = 576 times larger system...
|
|
||||||
orthogonal box = (0 0 0) to (22.572 60.192 22.572)
|
|
||||||
1 by 4 by 1 MPI processor grid
|
|
||||||
2304 atoms
|
|
||||||
replicate CPU = 0.000 seconds
|
|
||||||
|
|
||||||
region puck block INF INF INF 2 INF INF
|
|
||||||
set region puck type 2
|
|
||||||
Setting atom values ...
|
|
||||||
360 settings made for type
|
|
||||||
|
|
||||||
# Force Fields -----------------------------------
|
|
||||||
pair_style meam
|
|
||||||
pair_coeff * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
|
|
||||||
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
|
|
||||||
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
|
|
||||||
|
|
||||||
# Settings ---------------------------------------
|
|
||||||
timestep 0.002
|
|
||||||
thermo 100
|
|
||||||
|
|
||||||
# Computations -----------------------------------
|
|
||||||
compute voroN all voronoi/atom neighbors yes
|
|
||||||
|
|
||||||
run 0
|
|
||||||
WARNING: No fixes with time integration, atoms won't move
|
|
||||||
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
|
|
||||||
Neighbor list info ...
|
|
||||||
update: every = 1 steps, delay = 0 steps, check = yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 6.8
|
|
||||||
ghost atom cutoff = 6.8
|
|
||||||
binsize = 3.4, bins = 7 18 7
|
|
||||||
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
||||||
(1) pair meam, perpetual
|
|
||||||
attributes: full, newton on
|
|
||||||
pair build: full/bin/atomonly
|
|
||||||
stencil: full/bin/3d
|
|
||||||
bin: standard
|
|
||||||
(2) pair meam, perpetual, half/full from (1)
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: halffull/newton
|
|
||||||
stencil: none
|
|
||||||
bin: none
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
|
|
||||||
Step Temp E_pair E_mol TotEng Press
|
|
||||||
0 0 -9674.3728 0 -9674.3728 -212400.94
|
|
||||||
Loop time of 1.53e-06 on 4 procs for 0 steps with 2304 atoms
|
|
||||||
|
|
||||||
65.4% 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 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Other | | 1.53e-06 | | |100.00
|
|
||||||
|
|
||||||
Nlocal: 576 ave 576 max 576 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 2131 ave 2131 max 2131 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 24768 ave 24768 max 24768 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 49536 ave 49536 max 49536 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 198144
|
|
||||||
Ave neighs/atom = 86
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe
|
|
||||||
|
|
||||||
# Execution --------------------------------------
|
|
||||||
|
|
||||||
velocity all create 2400 908124 loop geom
|
|
||||||
fix temp all npt temp 1000 1000 1000 aniso 0 0 1
|
|
||||||
fix mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
|
|
||||||
thermo_style custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
|
|
||||||
#dump dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
|
|
||||||
|
|
||||||
run 1000
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
|
|
||||||
Step Temp Press Pxx Pyy Pzz Lx Ly Lz Volume PotEng f_mc[1] f_mc[2]
|
|
||||||
0 2400 -187517.52 -187464.47 -188202.62 -186885.48 22.572 60.192 22.572 30667.534 -9674.3728 0 0
|
|
||||||
100 1665.569 14271.813 14638.855 14316.569 13860.016 21.63675 57.721065 21.637799 27023.366 -9594.291 24 24
|
|
||||||
200 1598.6479 -6990.8349 -8574.1986 -5033.6147 -7364.6916 21.708963 58.123129 21.724821 27412.223 -9575.7322 48 47
|
|
||||||
300 1604.388 456.43285 1926.408 -1214.1721 657.0626 21.673369 58.090421 21.671716 27285.018 -9577.698 72 70
|
|
||||||
400 1601.1591 1303.6721 703.88473 1137.6607 2069.471 21.684004 58.049595 21.671161 27278.522 -9576.4811 96 94
|
|
||||||
500 1623.6044 -2243.2478 -2084.532 320.87709 -4966.0885 21.686171 58.097101 21.695911 27334.758 -9583.1878 120 118
|
|
||||||
600 1587.2041 421.60034 190.88741 -328.76599 1402.6796 21.712439 58.086039 21.655927 27312.229 -9572.559 144 141
|
|
||||||
700 1591.2923 32.327829 -2893.2353 1839.7574 1150.4614 21.719102 57.999862 21.666164 27292.974 -9573.9009 168 165
|
|
||||||
800 1580.8587 -105.51079 654.26389 -160.04168 -810.75457 21.670225 58.109245 21.684683 27306.229 -9570.6482 192 186
|
|
||||||
900 1570.7648 1290.088 1252.3689 255.62548 2362.2695 21.68101 58.100507 21.658755 27283.051 -9567.9864 216 209
|
|
||||||
1000 1598.1483 -125.35291 -3626.5479 3404.789 -154.29983 21.720146 57.952942 21.686111 27297.313 -9576.2975 240 231
|
|
||||||
Loop time of 9.17241 on 4 procs for 1000 steps with 2304 atoms
|
|
||||||
|
|
||||||
Performance: 18.839 ns/day, 1.274 hours/ns, 109.023 timesteps/s, 251.188 katom-step/s
|
|
||||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 7.7477 | 8.0143 | 8.1344 | 5.5 | 87.37
|
|
||||||
Neigh | 0.050543 | 0.056882 | 0.05986 | 1.6 | 0.62
|
|
||||||
Comm | 0.069784 | 0.16898 | 0.40996 | 34.2 | 1.84
|
|
||||||
Output | 0.00015612 | 0.0001707 | 0.00021249 | 0.0 | 0.00
|
|
||||||
Modify | 0.90628 | 0.93003 | 0.96157 | 2.2 | 10.14
|
|
||||||
Other | | 0.002053 | | | 0.02
|
|
||||||
|
|
||||||
Nlocal: 576 ave 614 max 505 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
||||||
Nghost: 2165.75 ave 2204 max 2132 min
|
|
||||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
|
||||||
Neighs: 32430.8 ave 35552 max 26564 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
||||||
FullNghs: 64861.5 ave 71111 max 53164 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
||||||
|
|
||||||
Total # of neighbors = 259446
|
|
||||||
Ave neighs/atom = 112.60677
|
|
||||||
Neighbor list builds = 62
|
|
||||||
Dangerous builds = 0
|
|
||||||
|
|
||||||
#write_data pulse_end.data
|
|
||||||
Total wall time: 0:00:09
|
|
||||||
@ -85,14 +85,24 @@ void PairMLIAPKokkos<DeviceType>::compute(int eflag, int vflag)
|
|||||||
error->all(FLERR, "Incompatible model and descriptor element count");
|
error->all(FLERR, "Incompatible model and descriptor element count");
|
||||||
|
|
||||||
ev_init(eflag, vflag, 0);
|
ev_init(eflag, vflag, 0);
|
||||||
if (eflag_atom && (int)k_eatom.h_view.extent(0) < maxeatom) {
|
if (eflag_atom) {
|
||||||
|
if ((int)k_eatom.h_view.extent(0) < maxeatom) {
|
||||||
memoryKK->destroy_kokkos(k_eatom,eatom);
|
memoryKK->destroy_kokkos(k_eatom,eatom);
|
||||||
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
|
memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
|
||||||
|
} else {
|
||||||
|
Kokkos::deep_copy(k_eatom.d_view,0);
|
||||||
|
k_eatom.modify<DeviceType>();
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if (vflag_atom && (int)k_vatom.h_view.extent(0) < maxeatom) {
|
if (vflag_atom) {
|
||||||
|
if ((int)k_vatom.h_view.extent(0) < maxeatom) {
|
||||||
memoryKK->destroy_kokkos(k_vatom,vatom);
|
memoryKK->destroy_kokkos(k_vatom,vatom);
|
||||||
memoryKK->create_kokkos(k_vatom,vatom,maxeatom,6,"pair:eatom");
|
memoryKK->create_kokkos(k_vatom,vatom,maxeatom,6,"pair:eatom");
|
||||||
|
} else {
|
||||||
|
Kokkos::deep_copy(k_vatom.d_view,0);
|
||||||
|
k_vatom.modify<DeviceType>();
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
data->generate_neighdata(list, eflag, vflag);
|
data->generate_neighdata(list, eflag, vflag);
|
||||||
|
|||||||
@ -1,921 +0,0 @@
|
|||||||
/* ----------------------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
Contributing authors: Jacob Tavenner
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#include "fix_neighbor_swap.h"
|
|
||||||
|
|
||||||
#include "angle.h"
|
|
||||||
#include "atom.h"
|
|
||||||
#include "bond.h"
|
|
||||||
#include "citeme.h"
|
|
||||||
#include "comm.h"
|
|
||||||
#include "compute.h"
|
|
||||||
#include "compute_voronoi_atom.h"
|
|
||||||
#include "dihedral.h"
|
|
||||||
#include "domain.h"
|
|
||||||
#include "error.h"
|
|
||||||
#include "fix.h"
|
|
||||||
#include "force.h"
|
|
||||||
#include "group.h"
|
|
||||||
#include "improper.h"
|
|
||||||
#include "kspace.h"
|
|
||||||
#include "math_extra.h"
|
|
||||||
#include "math_special.h"
|
|
||||||
#include "memory.h"
|
|
||||||
#include "modify.h"
|
|
||||||
#include "neighbor.h"
|
|
||||||
#include "pair.h"
|
|
||||||
#include "random_park.h"
|
|
||||||
#include "region.h"
|
|
||||||
#include "update.h"
|
|
||||||
|
|
||||||
#include <cfloat>
|
|
||||||
#include <cmath>
|
|
||||||
#include <cstring>
|
|
||||||
#include <unordered_set>
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
|
||||||
using namespace FixConst;
|
|
||||||
using MathExtra::distsq3;
|
|
||||||
using MathSpecial::square;
|
|
||||||
|
|
||||||
static const char cite_fix_neighbor_swap[] =
|
|
||||||
"fix neighbor/swap command: doi:10.1016/j.commatsci.2022.111929\n\n"
|
|
||||||
"@Article{Tavenner2023111929,\n"
|
|
||||||
" author = {Jacob P. Tavenner and Mikhail I. Mendelev and John W. Lawson},\n"
|
|
||||||
" title = {Molecular dynamics based kinetic Monte Carlo simulation for accelerated "
|
|
||||||
"diffusion},\n"
|
|
||||||
" journal = {Computational Materials Science},\n"
|
|
||||||
" year = {2023},\n"
|
|
||||||
" volume = {218},\n"
|
|
||||||
" pages = {111929}\n"
|
|
||||||
" url = {https://dx.doi.org/10.1016/j.commatsci.2022.111929}\n"
|
|
||||||
"}\n\n";
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
FixNeighborSwap::FixNeighborSwap(LAMMPS *lmp, int narg, char **arg) :
|
|
||||||
Fix(lmp, narg, arg), region(nullptr), idregion(nullptr), type_list(nullptr), rate_list(nullptr),
|
|
||||||
qtype(nullptr), sqrt_mass_ratio(nullptr), voro_neighbor_list(nullptr),
|
|
||||||
local_swap_iatom_list(nullptr), local_swap_neighbor_list(nullptr),
|
|
||||||
local_swap_type_list(nullptr), local_swap_probability(nullptr), random_equal(nullptr),
|
|
||||||
id_voro(nullptr), c_voro(nullptr), c_pe(nullptr)
|
|
||||||
{
|
|
||||||
if (narg < 10) utils::missing_cmd_args(FLERR, "fix neighbor/swap", error);
|
|
||||||
|
|
||||||
dynamic_group_allow = 1;
|
|
||||||
|
|
||||||
vector_flag = 1;
|
|
||||||
size_vector = 2;
|
|
||||||
global_freq = 1;
|
|
||||||
extvector = 0;
|
|
||||||
restart_global = 1;
|
|
||||||
time_depend = 1;
|
|
||||||
|
|
||||||
ke_flag = 1;
|
|
||||||
diff_flag = 0;
|
|
||||||
rates_flag = 0;
|
|
||||||
nswaptypes = 0;
|
|
||||||
|
|
||||||
if (lmp->citeme) lmp->citeme->add(cite_fix_neighbor_swap);
|
|
||||||
|
|
||||||
// required args
|
|
||||||
|
|
||||||
nevery = utils::inumeric(FLERR, arg[3], false, lmp);
|
|
||||||
ncycles = utils::inumeric(FLERR, arg[4], false, lmp);
|
|
||||||
seed = utils::inumeric(FLERR, arg[5], false, lmp);
|
|
||||||
double temperature = utils::numeric(FLERR, arg[6], false, lmp);
|
|
||||||
double r_0 = utils::inumeric(FLERR, arg[7], false, lmp);
|
|
||||||
|
|
||||||
if (nevery <= 0)
|
|
||||||
error->all(FLERR, 3, "Illegal fix neighbor/swap command nevery value: {}", nevery);
|
|
||||||
if (ncycles < 0)
|
|
||||||
error->all(FLERR, 4, "Illegal fix neighbor/swap command ncycles value: {}", ncycles);
|
|
||||||
if (seed <= 0) error->all(FLERR, 5, "Illegal fix neighbor/swap command seed value: {}", seed);
|
|
||||||
if (temperature <= 0.0)
|
|
||||||
error->all(FLERR, 6, "Illegal fix neighbor/swap command temperature value: {}", temperature);
|
|
||||||
if (r_0 <= 0.0) error->all(FLERR, 7, "Illegal fix neighbor/swap command R0 value: {}", r_0);
|
|
||||||
|
|
||||||
// Voro compute check
|
|
||||||
|
|
||||||
id_voro = utils::strdup(arg[8]);
|
|
||||||
c_voro = modify->get_compute_by_id(id_voro);
|
|
||||||
if (!c_voro) error->all(FLERR, 8, "Could not find compute voronoi ID {}", id_voro);
|
|
||||||
if (c_voro->local_flag == 0)
|
|
||||||
error->all(FLERR, 8, "Voronoi compute {} does not compute local info", id_voro);
|
|
||||||
if (c_voro->size_local_cols != 3)
|
|
||||||
error->all(FLERR, 8, "Voronoi compute {} does not compute i, j, sizes as expected", id_voro);
|
|
||||||
|
|
||||||
beta = 1.0 / (force->boltz * temperature);
|
|
||||||
inv_r_0 = 1.0 / r_0;
|
|
||||||
|
|
||||||
memory->create(type_list, atom->ntypes, "neighbor/swap:type_list");
|
|
||||||
memory->create(rate_list, atom->ntypes, "neighbor/swap:rate_list");
|
|
||||||
|
|
||||||
// read options from end of input line
|
|
||||||
|
|
||||||
options(narg - 9, &arg[9]);
|
|
||||||
|
|
||||||
// random number generator, same for all procs
|
|
||||||
|
|
||||||
random_equal = new RanPark(lmp, seed);
|
|
||||||
|
|
||||||
// set up reneighboring
|
|
||||||
|
|
||||||
force_reneighbor = 1;
|
|
||||||
next_reneighbor = update->ntimestep + 1;
|
|
||||||
|
|
||||||
// zero out counters
|
|
||||||
|
|
||||||
nswap_attempts = 0.0;
|
|
||||||
nswap_successes = 0.0;
|
|
||||||
|
|
||||||
atom_swap_nmax = 0;
|
|
||||||
|
|
||||||
// set comm size needed by this Fix
|
|
||||||
|
|
||||||
if (atom->q_flag)
|
|
||||||
comm_forward = 2;
|
|
||||||
else
|
|
||||||
comm_forward = 1;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
FixNeighborSwap::~FixNeighborSwap()
|
|
||||||
{
|
|
||||||
memory->destroy(type_list);
|
|
||||||
memory->destroy(rate_list);
|
|
||||||
memory->destroy(qtype);
|
|
||||||
memory->destroy(sqrt_mass_ratio);
|
|
||||||
memory->destroy(local_swap_iatom_list);
|
|
||||||
memory->destroy(local_swap_neighbor_list);
|
|
||||||
memory->destroy(local_swap_probability);
|
|
||||||
memory->destroy(local_swap_type_list);
|
|
||||||
delete[] idregion;
|
|
||||||
delete[] id_voro;
|
|
||||||
delete random_equal;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
parse optional parameters at end of input line
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
static const std::unordered_set<std::string> known_keywords = {"region", "ke", "types", "diff",
|
|
||||||
"rates"};
|
|
||||||
static bool is_keyword(const std::string &arg)
|
|
||||||
{
|
|
||||||
return known_keywords.find(arg) != known_keywords.end();
|
|
||||||
}
|
|
||||||
|
|
||||||
void FixNeighborSwap::options(int narg, char **arg)
|
|
||||||
{
|
|
||||||
if (narg < 0) utils::missing_cmd_args(FLERR, "fix neighbor/swap", error);
|
|
||||||
|
|
||||||
int ioffset = 9; // first 9 arguments are fixed and handled in constructor
|
|
||||||
int iarg = 0;
|
|
||||||
while (iarg < narg) {
|
|
||||||
if (strcmp(arg[iarg], "region") == 0) {
|
|
||||||
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix neighbor/swap region", error);
|
|
||||||
delete[] idregion;
|
|
||||||
idregion = utils::strdup(arg[iarg + 1]);
|
|
||||||
region = domain->get_region_by_id(idregion);
|
|
||||||
if (!region)
|
|
||||||
error->all(FLERR, iarg + 1 + ioffset, "Region ID {} for fix neighbor/swap does not exist",
|
|
||||||
idregion);
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg], "ke") == 0) {
|
|
||||||
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix neighbor/swap ke", error);
|
|
||||||
ke_flag = utils::logical(FLERR, arg[iarg + 1], false, lmp);
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg], "types") == 0) {
|
|
||||||
if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "fix neighbor/swap types", error);
|
|
||||||
if (diff_flag)
|
|
||||||
error->all(FLERR, iarg + ioffset, "Cannot use 'diff' and 'types' keywords together");
|
|
||||||
iarg++;
|
|
||||||
nswaptypes = 0;
|
|
||||||
while (iarg < narg) {
|
|
||||||
if (is_keyword(arg[iarg])) break;
|
|
||||||
if (nswaptypes >= atom->ntypes)
|
|
||||||
error->all(FLERR, iarg + ioffset, "Too many arguments to fix neighbor/swap types");
|
|
||||||
type_list[nswaptypes] = utils::expand_type_int(FLERR, arg[iarg], Atom::ATOM, lmp);
|
|
||||||
nswaptypes++;
|
|
||||||
iarg++;
|
|
||||||
}
|
|
||||||
} else if (strcmp(arg[iarg], "diff") == 0) {
|
|
||||||
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix neighbor/swap diff", error);
|
|
||||||
if (diff_flag) error->all(FLERR, iarg + ioffset, "Cannot use 'diff' keyword multiple times");
|
|
||||||
if (nswaptypes != 0)
|
|
||||||
error->all(FLERR, iarg + ioffset, "Cannot use 'diff' and 'types' keywords together");
|
|
||||||
type_list[nswaptypes] = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
|
|
||||||
diff_flag = 1;
|
|
||||||
nswaptypes++;
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg], "rates") == 0) {
|
|
||||||
if (iarg + atom->ntypes >= narg)
|
|
||||||
utils::missing_cmd_args(FLERR, "fix neighbor/swap rates", error);
|
|
||||||
iarg++;
|
|
||||||
int i = 0;
|
|
||||||
while (iarg < narg) {
|
|
||||||
if (is_keyword(arg[iarg])) break;
|
|
||||||
if (i >= atom->ntypes) error->all(FLERR, "Too many values for fix neighbor/swap rates");
|
|
||||||
rate_list[i] = utils::numeric(FLERR, arg[iarg], false, lmp);
|
|
||||||
i++;
|
|
||||||
iarg++;
|
|
||||||
}
|
|
||||||
rates_flag = 1;
|
|
||||||
if (i != atom->ntypes)
|
|
||||||
error->all(FLERR, "Fix neighbor/swap rates keyword must have exactly {} arguments",
|
|
||||||
atom->ntypes);
|
|
||||||
} else {
|
|
||||||
error->all(FLERR, "Unknown fix neighbor/swap keyword: {}", arg[iarg]);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// checks
|
|
||||||
if (!nswaptypes && !diff_flag)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE,
|
|
||||||
"Must specify at either 'types' or 'diff' keyword with fix neighbor/swap");
|
|
||||||
|
|
||||||
if (nswaptypes < 2 && !diff_flag)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE,
|
|
||||||
"Must specify at least 2 atom types in fix neighbor/swap 'types' keyword");
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
int FixNeighborSwap::setmask()
|
|
||||||
{
|
|
||||||
int mask = 0;
|
|
||||||
mask |= PRE_EXCHANGE;
|
|
||||||
return mask;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixNeighborSwap::init()
|
|
||||||
{
|
|
||||||
c_pe = modify->get_compute_by_id("thermo_pe");
|
|
||||||
if (!c_pe) error->all(FLERR, Error::NOLASTLINE, "Could not find 'thermo_pe' compute");
|
|
||||||
|
|
||||||
c_voro = modify->get_compute_by_id(id_voro);
|
|
||||||
if (!c_voro)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE, "Could not find compute voronoi ID {}", id_voro);
|
|
||||||
|
|
||||||
// set index and check validity of region
|
|
||||||
|
|
||||||
if (idregion) {
|
|
||||||
region = domain->get_region_by_id(idregion);
|
|
||||||
if (!region)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE, "Region {} for fix neighbor/swap does not exist",
|
|
||||||
idregion);
|
|
||||||
}
|
|
||||||
|
|
||||||
for (int iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
|
|
||||||
if (type_list[iswaptype] <= 0 || type_list[iswaptype] > atom->ntypes)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE, "Invalid atom type in fix neighbor/swap command");
|
|
||||||
|
|
||||||
int *type = atom->type;
|
|
||||||
if (atom->q_flag) {
|
|
||||||
double qmax, qmin;
|
|
||||||
int firstall, first;
|
|
||||||
memory->create(qtype, nswaptypes, "neighbor/swap:qtype");
|
|
||||||
for (int iswaptype = 0; iswaptype < nswaptypes; iswaptype++) {
|
|
||||||
first = 1;
|
|
||||||
for (int i = 0; i < atom->nlocal; i++) {
|
|
||||||
if (atom->mask[i] & groupbit) {
|
|
||||||
if (type[i] == type_list[iswaptype]) {
|
|
||||||
if (first > 0) {
|
|
||||||
qtype[iswaptype] = atom->q[i];
|
|
||||||
first = 0;
|
|
||||||
} else if (qtype[iswaptype] != atom->q[i])
|
|
||||||
first = -1;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
MPI_Allreduce(&first, &firstall, 1, MPI_INT, MPI_MIN, world);
|
|
||||||
if (firstall < 0)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE,
|
|
||||||
"All atoms of a swapped type must have the same charge");
|
|
||||||
if (firstall > 0)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE,
|
|
||||||
"At least one atom of each swapped type must be present to define charges");
|
|
||||||
if (first) qtype[iswaptype] = -DBL_MAX;
|
|
||||||
MPI_Allreduce(&qtype[iswaptype], &qmax, 1, MPI_DOUBLE, MPI_MAX, world);
|
|
||||||
if (first) qtype[iswaptype] = DBL_MAX;
|
|
||||||
MPI_Allreduce(&qtype[iswaptype], &qmin, 1, MPI_DOUBLE, MPI_MIN, world);
|
|
||||||
if (qmax != qmin)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE, "All atoms of a swapped type must have same charge.");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
memory->create(sqrt_mass_ratio, atom->ntypes + 1, atom->ntypes + 1,
|
|
||||||
"neighbor/swap:sqrt_mass_ratio");
|
|
||||||
for (int itype = 1; itype <= atom->ntypes; itype++)
|
|
||||||
for (int jtype = 1; jtype <= atom->ntypes; jtype++)
|
|
||||||
sqrt_mass_ratio[itype][jtype] = sqrt(atom->mass[itype] / atom->mass[jtype]);
|
|
||||||
|
|
||||||
// check to see if itype and jtype cutoffs are the same
|
|
||||||
// if not, reneighboring will be needed between swaps
|
|
||||||
|
|
||||||
double **cutsq = force->pair->cutsq;
|
|
||||||
unequal_cutoffs = false;
|
|
||||||
for (int iswaptype = 0; iswaptype < nswaptypes; iswaptype++)
|
|
||||||
for (int jswaptype = 0; jswaptype < nswaptypes; jswaptype++)
|
|
||||||
for (int ktype = 1; ktype <= atom->ntypes; ktype++)
|
|
||||||
if (cutsq[type_list[iswaptype]][ktype] != cutsq[type_list[jswaptype]][ktype])
|
|
||||||
unequal_cutoffs = true;
|
|
||||||
|
|
||||||
// check that no swappable atoms are in atom->firstgroup
|
|
||||||
// swapping such an atom might not leave firstgroup atoms first
|
|
||||||
|
|
||||||
if (atom->firstgroup >= 0) {
|
|
||||||
int *mask = atom->mask;
|
|
||||||
int firstgroupbit = group->bitmask[atom->firstgroup];
|
|
||||||
|
|
||||||
int flag = 0;
|
|
||||||
for (int i = 0; i < atom->nlocal; i++)
|
|
||||||
if ((mask[i] == groupbit) && (mask[i] && firstgroupbit)) flag = 1;
|
|
||||||
|
|
||||||
int flagall;
|
|
||||||
MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world);
|
|
||||||
if (flagall)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE,
|
|
||||||
"Cannot use fix neighbor/swap on atoms in atom_modify first group");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
attempt Monte Carlo swaps
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixNeighborSwap::pre_exchange()
|
|
||||||
{
|
|
||||||
// just return if should not be called on this timestep
|
|
||||||
|
|
||||||
if (next_reneighbor != update->ntimestep) return;
|
|
||||||
|
|
||||||
// ensure current system is ready to compute energy
|
|
||||||
|
|
||||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
|
||||||
domain->pbc();
|
|
||||||
comm->exchange();
|
|
||||||
comm->borders();
|
|
||||||
if (domain->triclinic) domain->lamda2x(atom->nlocal + atom->nghost);
|
|
||||||
if (modify->n_pre_neighbor) modify->pre_neighbor();
|
|
||||||
neighbor->build(1);
|
|
||||||
|
|
||||||
// energy_stored = energy of current state
|
|
||||||
// will be updated after accepted swaps
|
|
||||||
|
|
||||||
energy_stored = energy_full();
|
|
||||||
|
|
||||||
// attempt Ncycle atom swaps
|
|
||||||
|
|
||||||
int nsuccess = 0;
|
|
||||||
update_iswap_atoms_list();
|
|
||||||
for (int i = 0; i < ncycles; i++) nsuccess += attempt_swap();
|
|
||||||
|
|
||||||
// udpate MC stats
|
|
||||||
|
|
||||||
nswap_attempts += ncycles;
|
|
||||||
nswap_successes += nsuccess;
|
|
||||||
|
|
||||||
next_reneighbor = update->ntimestep + nevery;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
attempt a swap of a pair of atoms
|
|
||||||
compare before/after energy and accept/reject the swap
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
int FixNeighborSwap::attempt_swap()
|
|
||||||
{
|
|
||||||
if (niswap == 0) return 0;
|
|
||||||
|
|
||||||
// pre-swap energy
|
|
||||||
|
|
||||||
double energy_before = energy_stored;
|
|
||||||
|
|
||||||
// pick a random atom i
|
|
||||||
|
|
||||||
int i = pick_i_swap_atom();
|
|
||||||
|
|
||||||
// build nearest-neighbor list based on atom i
|
|
||||||
|
|
||||||
build_i_neighbor_list(i);
|
|
||||||
if (njswap <= 0) return 0;
|
|
||||||
|
|
||||||
// pick a neighbor atom j based on i neighbor list
|
|
||||||
jtype_selected = -1;
|
|
||||||
int j = pick_j_swap_neighbor();
|
|
||||||
|
|
||||||
int itype = type_list[0];
|
|
||||||
int jtype = jtype_selected;
|
|
||||||
|
|
||||||
// Accept swap if types are equal, no change to system
|
|
||||||
if (itype == jtype) { return 1; }
|
|
||||||
|
|
||||||
// swap their properties
|
|
||||||
if (i >= 0) {
|
|
||||||
atom->type[i] = jtype;
|
|
||||||
if (atom->q_flag) atom->q[i] = qtype[jtype_selected];
|
|
||||||
}
|
|
||||||
if (j >= 0) {
|
|
||||||
atom->type[j] = itype;
|
|
||||||
if (atom->q_flag) atom->q[j] = qtype[0];
|
|
||||||
}
|
|
||||||
|
|
||||||
// if unequal_cutoffs, call comm->borders() and rebuild neighbor list
|
|
||||||
// else communicate ghost atoms
|
|
||||||
// call to comm->exchange() is a no-op but clears ghost atoms
|
|
||||||
|
|
||||||
if (unequal_cutoffs) {
|
|
||||||
if (domain->triclinic) domain->x2lamda(atom->nlocal);
|
|
||||||
domain->pbc();
|
|
||||||
comm->exchange();
|
|
||||||
comm->borders();
|
|
||||||
if (domain->triclinic) domain->lamda2x(atom->nlocal + atom->nghost);
|
|
||||||
if (modify->n_pre_neighbor) modify->pre_neighbor();
|
|
||||||
neighbor->build(1);
|
|
||||||
} else {
|
|
||||||
comm->forward_comm(this);
|
|
||||||
}
|
|
||||||
|
|
||||||
// post-swap energy
|
|
||||||
|
|
||||||
double energy_after = energy_full();
|
|
||||||
|
|
||||||
// if swap accepted, return 1
|
|
||||||
// if ke_flag, rescale atom velocities
|
|
||||||
|
|
||||||
if (random_equal->uniform() < exp(beta * (energy_before - energy_after))) {
|
|
||||||
update_iswap_atoms_list();
|
|
||||||
if (ke_flag) {
|
|
||||||
if (i >= 0) {
|
|
||||||
atom->v[i][0] *= sqrt_mass_ratio[itype][jtype];
|
|
||||||
atom->v[i][1] *= sqrt_mass_ratio[itype][jtype];
|
|
||||||
atom->v[i][2] *= sqrt_mass_ratio[itype][jtype];
|
|
||||||
}
|
|
||||||
if (j >= 0) {
|
|
||||||
atom->v[j][0] *= sqrt_mass_ratio[jtype][itype];
|
|
||||||
atom->v[j][1] *= sqrt_mass_ratio[jtype][itype];
|
|
||||||
atom->v[j][2] *= sqrt_mass_ratio[jtype][itype];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
energy_stored = energy_after;
|
|
||||||
return 1;
|
|
||||||
}
|
|
||||||
|
|
||||||
// swap not accepted, return 0
|
|
||||||
// restore the swapped itype & jtype atoms
|
|
||||||
// do not need to re-call comm->borders() and rebuild neighbor list
|
|
||||||
// since will be done on next cycle or in Verlet when this fix finishes
|
|
||||||
|
|
||||||
if (i >= 0) {
|
|
||||||
atom->type[i] = itype;
|
|
||||||
if (atom->q_flag) atom->q[i] = qtype[0];
|
|
||||||
}
|
|
||||||
if (j >= 0) {
|
|
||||||
atom->type[j] = jtype;
|
|
||||||
if (atom->q_flag) atom->q[j] = qtype[jtype_selected];
|
|
||||||
}
|
|
||||||
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
compute system potential energy
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double FixNeighborSwap::energy_full()
|
|
||||||
{
|
|
||||||
int eflag = 1;
|
|
||||||
int vflag = 0;
|
|
||||||
|
|
||||||
if (modify->n_pre_force) modify->pre_force(vflag);
|
|
||||||
|
|
||||||
if (force->pair) force->pair->compute(eflag, vflag);
|
|
||||||
|
|
||||||
if (atom->molecular != Atom::ATOMIC) {
|
|
||||||
if (force->bond) force->bond->compute(eflag, vflag);
|
|
||||||
if (force->angle) force->angle->compute(eflag, vflag);
|
|
||||||
if (force->dihedral) force->dihedral->compute(eflag, vflag);
|
|
||||||
if (force->improper) force->improper->compute(eflag, vflag);
|
|
||||||
}
|
|
||||||
|
|
||||||
if (force->kspace) force->kspace->compute(eflag, vflag);
|
|
||||||
|
|
||||||
if (modify->n_post_force_any) modify->post_force(vflag);
|
|
||||||
|
|
||||||
update->eflag_global = update->ntimestep;
|
|
||||||
double total_energy = c_pe->compute_scalar();
|
|
||||||
|
|
||||||
return total_energy;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
int FixNeighborSwap::pick_i_swap_atom()
|
|
||||||
{
|
|
||||||
tagint *id = atom->tag;
|
|
||||||
int i = -1;
|
|
||||||
|
|
||||||
int iwhichglobal = static_cast<int>(niswap * random_equal->uniform());
|
|
||||||
if ((iwhichglobal >= niswap_before) && (iwhichglobal < niswap_before + niswap_local)) {
|
|
||||||
int iwhichlocal = iwhichglobal - niswap_before;
|
|
||||||
i = local_swap_iatom_list[iwhichlocal];
|
|
||||||
MPI_Allreduce(&id[i], &id_center, 1, MPI_INT, MPI_MAX, world);
|
|
||||||
} else {
|
|
||||||
id_center = -1;
|
|
||||||
}
|
|
||||||
return i;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
int FixNeighborSwap::pick_j_swap_neighbor()
|
|
||||||
{
|
|
||||||
int j = -1;
|
|
||||||
int jtype_selected_local = -1;
|
|
||||||
|
|
||||||
// Generate random double from 0 to maximum global probability
|
|
||||||
double selected_prob = static_cast<double>(global_probability * random_equal->uniform());
|
|
||||||
|
|
||||||
// Find which local swap atom corresponds to probability
|
|
||||||
if ((selected_prob >= prev_probability) &&
|
|
||||||
(selected_prob < prev_probability + local_probability)) {
|
|
||||||
double search_prob = selected_prob - prev_probability;
|
|
||||||
for (int n = 0; n < njswap_local; n++) {
|
|
||||||
if (search_prob > local_swap_probability[n]) {
|
|
||||||
search_prob -= local_swap_probability[n];
|
|
||||||
} else {
|
|
||||||
j = local_swap_neighbor_list[n];
|
|
||||||
jtype_selected_local = local_swap_type_list[n];
|
|
||||||
MPI_Allreduce(&jtype_selected_local, &jtype_selected, 1, MPI_INT, MPI_MAX, world);
|
|
||||||
return j;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
error->all(FLERR, Error::NOLASTLINE, "Did not select local neighbor swap atom");
|
|
||||||
}
|
|
||||||
|
|
||||||
MPI_Allreduce(&jtype_selected_local, &jtype_selected, 1, MPI_INT, MPI_MAX, world);
|
|
||||||
return j;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixNeighborSwap::build_i_neighbor_list(int i_center)
|
|
||||||
{
|
|
||||||
int nghost = atom->nghost;
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
int *type = atom->type;
|
|
||||||
double **x = atom->x;
|
|
||||||
tagint *id = atom->tag;
|
|
||||||
|
|
||||||
// Allocate local_swap_neighbor_list size
|
|
||||||
|
|
||||||
memory->sfree(local_swap_neighbor_list);
|
|
||||||
atom_swap_nmax = atom->nmax;
|
|
||||||
local_swap_neighbor_list =
|
|
||||||
(int *) memory->smalloc(atom_swap_nmax * sizeof(int), "MCSWAP:local_swap_neighbor_list");
|
|
||||||
|
|
||||||
memory->sfree(local_swap_probability);
|
|
||||||
local_swap_probability = (double *) memory->smalloc(atom_swap_nmax * sizeof(double),
|
|
||||||
"MCSWAP:local_swap_probability_list");
|
|
||||||
|
|
||||||
memory->sfree(local_swap_type_list);
|
|
||||||
local_swap_type_list =
|
|
||||||
(int *) memory->smalloc(atom_swap_nmax * sizeof(int), "MCSWAP:local_swap_type_list");
|
|
||||||
|
|
||||||
// Compute voronoi and access neighbor list
|
|
||||||
|
|
||||||
c_voro->compute_local();
|
|
||||||
|
|
||||||
voro_neighbor_list = c_voro->array_local;
|
|
||||||
njswap_local = 0;
|
|
||||||
local_probability = 0.0;
|
|
||||||
|
|
||||||
for (int n = 0; n < c_voro->size_local_rows; n++) {
|
|
||||||
|
|
||||||
int temp_j_id = -1;
|
|
||||||
int temp_j = -1;
|
|
||||||
|
|
||||||
// Find local voronoi entry with selected central atom
|
|
||||||
if ((int) voro_neighbor_list[n][0] == id_center) {
|
|
||||||
temp_j_id = voro_neighbor_list[n][1];
|
|
||||||
temp_j = -1;
|
|
||||||
} else if (((int) voro_neighbor_list[n][1] == id_center) && (i_center < 0)) {
|
|
||||||
temp_j_id = voro_neighbor_list[n][0];
|
|
||||||
temp_j = -1;
|
|
||||||
} else {
|
|
||||||
continue;
|
|
||||||
}
|
|
||||||
|
|
||||||
// Find which local atom corresponds to neighbor
|
|
||||||
for (int j = 0; j < nlocal; j++) {
|
|
||||||
if (temp_j_id == id[j]) {
|
|
||||||
temp_j = j;
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// If temp_j not on this processor, skip
|
|
||||||
if (temp_j < 0) continue;
|
|
||||||
|
|
||||||
if (region) {
|
|
||||||
if (region->match(x[temp_j][0], x[temp_j][1], x[temp_j][2]) == 1) {
|
|
||||||
if (atom->mask[temp_j] & groupbit) {
|
|
||||||
if (diff_flag) {
|
|
||||||
// Calculate distance from i to each j, adjust probability of selection
|
|
||||||
|
|
||||||
// Get distance if own center atom
|
|
||||||
double r = INFINITY;
|
|
||||||
|
|
||||||
// Get local id of ghost center atom when ghost
|
|
||||||
for (int i = nlocal; i < nlocal + nghost; i++) {
|
|
||||||
double rtmp = sqrt(distsq3(x[temp_j], x[i]));
|
|
||||||
if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (rates_flag) {
|
|
||||||
local_swap_probability[njswap_local] =
|
|
||||||
rate_list[type[temp_j] - 1] * exp(-square(r * inv_r_0));
|
|
||||||
} else {
|
|
||||||
local_swap_probability[njswap_local] = exp(-square(r * inv_r_0));
|
|
||||||
}
|
|
||||||
local_probability += local_swap_probability[njswap_local];
|
|
||||||
local_swap_type_list[njswap_local] = type[temp_j];
|
|
||||||
local_swap_neighbor_list[njswap_local] = temp_j;
|
|
||||||
njswap_local++;
|
|
||||||
} else {
|
|
||||||
for (int jswaptype = 1; jswaptype < nswaptypes; jswaptype++) {
|
|
||||||
if (type[temp_j] == type_list[jswaptype]) {
|
|
||||||
// Calculate distance from i to each j, adjust probability of selection
|
|
||||||
// Get distance if own center atom
|
|
||||||
double r = INFINITY;
|
|
||||||
|
|
||||||
// Get local id of ghost center atom when ghost
|
|
||||||
for (int i = nlocal; i < nlocal + nghost; i++) {
|
|
||||||
double rtmp = sqrt(distsq3(x[temp_j], x[i]));
|
|
||||||
if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (rates_flag) {
|
|
||||||
local_swap_probability[njswap_local] =
|
|
||||||
rate_list[type[temp_j] - 1] * exp(-square(r * inv_r_0));
|
|
||||||
} else {
|
|
||||||
local_swap_probability[njswap_local] = exp(-square(r * inv_r_0));
|
|
||||||
}
|
|
||||||
local_probability += local_swap_probability[njswap_local];
|
|
||||||
|
|
||||||
local_swap_type_list[njswap_local] = jswaptype;
|
|
||||||
local_swap_neighbor_list[njswap_local] = temp_j;
|
|
||||||
njswap_local++;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
} else {
|
|
||||||
if (atom->mask[temp_j] & groupbit) {
|
|
||||||
if (diff_flag) {
|
|
||||||
// Calculate distance from i to each j, adjust probability of selection
|
|
||||||
// Get distance if own center atom
|
|
||||||
double r = INFINITY;
|
|
||||||
|
|
||||||
// Get local id of ghost center atoms
|
|
||||||
for (int i = nlocal; i < nlocal + nghost; i++) {
|
|
||||||
double rtmp = sqrt(distsq3(x[temp_j], x[i]));
|
|
||||||
if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (rates_flag) {
|
|
||||||
local_swap_probability[njswap_local] =
|
|
||||||
rate_list[type[temp_j] - 1] * exp(-square(r * inv_r_0));
|
|
||||||
} else {
|
|
||||||
local_swap_probability[njswap_local] = exp(-square(r * inv_r_0));
|
|
||||||
}
|
|
||||||
local_probability += local_swap_probability[njswap_local];
|
|
||||||
|
|
||||||
local_swap_type_list[njswap_local] = type[temp_j];
|
|
||||||
local_swap_neighbor_list[njswap_local] = temp_j;
|
|
||||||
njswap_local++;
|
|
||||||
} else {
|
|
||||||
for (int jswaptype = 1; jswaptype < nswaptypes; jswaptype++) {
|
|
||||||
if (type[temp_j] == type_list[jswaptype]) {
|
|
||||||
// Calculate distance from i to each j, adjust probability of selection
|
|
||||||
// Get distance if own center atom
|
|
||||||
double r = INFINITY;
|
|
||||||
|
|
||||||
// Get local id of ghost center atom when ghost
|
|
||||||
for (int i = nlocal; i < nlocal + nghost; i++) {
|
|
||||||
double rtmp = sqrt(distsq3(x[temp_j], x[i]));
|
|
||||||
if ((id[i] == id_center) && (rtmp < r)) r = rtmp;
|
|
||||||
}
|
|
||||||
|
|
||||||
if (rates_flag) {
|
|
||||||
local_swap_probability[njswap_local] =
|
|
||||||
rate_list[type[temp_j] - 1] * exp(-square(r * inv_r_0));
|
|
||||||
} else {
|
|
||||||
local_swap_probability[njswap_local] = exp(-square(r * inv_r_0));
|
|
||||||
}
|
|
||||||
local_probability += local_swap_probability[njswap_local];
|
|
||||||
|
|
||||||
local_swap_type_list[njswap_local] = jswaptype;
|
|
||||||
local_swap_neighbor_list[njswap_local] = temp_j;
|
|
||||||
njswap_local++;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
MPI_Allreduce(&njswap_local, &njswap, 1, MPI_INT, MPI_SUM, world);
|
|
||||||
MPI_Scan(&njswap_local, &njswap_before, 1, MPI_INT, MPI_SUM, world);
|
|
||||||
njswap_before -= njswap_local;
|
|
||||||
|
|
||||||
MPI_Allreduce(&local_probability, &global_probability, 1, MPI_DOUBLE, MPI_SUM, world);
|
|
||||||
MPI_Scan(&local_probability, &prev_probability, 1, MPI_DOUBLE, MPI_SUM, world);
|
|
||||||
prev_probability -= local_probability;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
update the list of swap atoms
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixNeighborSwap::update_iswap_atoms_list()
|
|
||||||
{
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
int *type = atom->type;
|
|
||||||
double **x = atom->x;
|
|
||||||
|
|
||||||
if (atom->nmax > atom_swap_nmax) {
|
|
||||||
memory->sfree(local_swap_iatom_list);
|
|
||||||
atom_swap_nmax = atom->nmax;
|
|
||||||
local_swap_iatom_list =
|
|
||||||
(int *) memory->smalloc(atom_swap_nmax * sizeof(int), "MCSWAP:local_swap_iatom_list");
|
|
||||||
}
|
|
||||||
|
|
||||||
niswap_local = 0;
|
|
||||||
|
|
||||||
if (region) {
|
|
||||||
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
if (region->match(x[i][0], x[i][1], x[i][2]) == 1) {
|
|
||||||
if (atom->mask[i] & groupbit) {
|
|
||||||
if (type[i] == type_list[0]) {
|
|
||||||
local_swap_iatom_list[niswap_local] = i;
|
|
||||||
niswap_local++;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
} else {
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
if (atom->mask[i] & groupbit) {
|
|
||||||
if (type[i] == type_list[0]) {
|
|
||||||
local_swap_iatom_list[niswap_local] = i;
|
|
||||||
niswap_local++;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
MPI_Allreduce(&niswap_local, &niswap, 1, MPI_INT, MPI_SUM, world);
|
|
||||||
MPI_Scan(&niswap_local, &niswap_before, 1, MPI_INT, MPI_SUM, world);
|
|
||||||
niswap_before -= niswap_local;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
int FixNeighborSwap::pack_forward_comm(int n, int *list, double *buf, int /*pbc_flag*/,
|
|
||||||
int * /*pbc*/)
|
|
||||||
{
|
|
||||||
int i, j, m;
|
|
||||||
|
|
||||||
int *type = atom->type;
|
|
||||||
double *q = atom->q;
|
|
||||||
|
|
||||||
m = 0;
|
|
||||||
|
|
||||||
if (atom->q_flag) {
|
|
||||||
for (i = 0; i < n; i++) {
|
|
||||||
j = list[i];
|
|
||||||
buf[m++] = type[j];
|
|
||||||
buf[m++] = q[j];
|
|
||||||
}
|
|
||||||
} else {
|
|
||||||
for (i = 0; i < n; i++) {
|
|
||||||
j = list[i];
|
|
||||||
buf[m++] = type[j];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
return m;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixNeighborSwap::unpack_forward_comm(int n, int first, double *buf)
|
|
||||||
{
|
|
||||||
int i, m, last;
|
|
||||||
|
|
||||||
int *type = atom->type;
|
|
||||||
double *q = atom->q;
|
|
||||||
|
|
||||||
m = 0;
|
|
||||||
last = first + n;
|
|
||||||
|
|
||||||
if (atom->q_flag) {
|
|
||||||
for (i = first; i < last; i++) {
|
|
||||||
type[i] = static_cast<int>(buf[m++]);
|
|
||||||
q[i] = buf[m++];
|
|
||||||
}
|
|
||||||
} else {
|
|
||||||
for (i = first; i < last; i++) type[i] = static_cast<int>(buf[m++]);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
return acceptance ratio
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double FixNeighborSwap::compute_vector(int n)
|
|
||||||
{
|
|
||||||
if (n == 0) return nswap_attempts;
|
|
||||||
if (n == 1) return nswap_successes;
|
|
||||||
return 0.0;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
memory usage of local atom-based arrays
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double FixNeighborSwap::memory_usage()
|
|
||||||
{
|
|
||||||
double bytes = (double) atom_swap_nmax * sizeof(int);
|
|
||||||
return bytes;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
pack entire state of Fix into one write
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixNeighborSwap::write_restart(FILE *fp)
|
|
||||||
{
|
|
||||||
int n = 0;
|
|
||||||
double list[6];
|
|
||||||
list[n++] = random_equal->state();
|
|
||||||
list[n++] = ubuf(next_reneighbor).d;
|
|
||||||
list[n++] = nswap_attempts;
|
|
||||||
list[n++] = nswap_successes;
|
|
||||||
list[n++] = ubuf(update->ntimestep).d;
|
|
||||||
|
|
||||||
if (comm->me == 0) {
|
|
||||||
int size = n * sizeof(double);
|
|
||||||
fwrite(&size, sizeof(int), 1, fp);
|
|
||||||
fwrite(list, sizeof(double), n, fp);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
use state info from restart file to restart the Fix
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixNeighborSwap::restart(char *buf)
|
|
||||||
{
|
|
||||||
int n = 0;
|
|
||||||
double *list = (double *) buf;
|
|
||||||
|
|
||||||
seed = static_cast<int>(list[n++]);
|
|
||||||
random_equal->reset(seed);
|
|
||||||
|
|
||||||
next_reneighbor = (bigint) ubuf(list[n++]).i;
|
|
||||||
|
|
||||||
nswap_attempts = static_cast<int>(list[n++]);
|
|
||||||
nswap_successes = static_cast<int>(list[n++]);
|
|
||||||
|
|
||||||
bigint ntimestep_restart = (bigint) ubuf(list[n++]).i;
|
|
||||||
if (ntimestep_restart != update->ntimestep)
|
|
||||||
error->all(FLERR, Error::NOLASTLINE,
|
|
||||||
"Must not reset timestep when restarting fix neighbor/swap");
|
|
||||||
}
|
|
||||||
@ -1,98 +0,0 @@
|
|||||||
/* -*- c++ -*- ----------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#ifdef FIX_CLASS
|
|
||||||
// clang-format off
|
|
||||||
FixStyle(neighbor/swap,FixNeighborSwap);
|
|
||||||
// clang-format on
|
|
||||||
#else
|
|
||||||
|
|
||||||
#ifndef LMP_FIX_NEIGH_SWAP_H
|
|
||||||
#define LMP_FIX_NEIGH_SWAP_H
|
|
||||||
|
|
||||||
#include "fix.h"
|
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
|
||||||
|
|
||||||
class FixNeighborSwap : public Fix {
|
|
||||||
public:
|
|
||||||
FixNeighborSwap(class LAMMPS *, int, char **);
|
|
||||||
~FixNeighborSwap();
|
|
||||||
int setmask();
|
|
||||||
void init();
|
|
||||||
void pre_exchange();
|
|
||||||
int pack_forward_comm(int, int *, double *, int, int *);
|
|
||||||
void unpack_forward_comm(int, int, double *);
|
|
||||||
double compute_vector(int);
|
|
||||||
double memory_usage();
|
|
||||||
void write_restart(FILE *);
|
|
||||||
void restart(char *);
|
|
||||||
|
|
||||||
private:
|
|
||||||
int nevery, seed;
|
|
||||||
int ke_flag; // yes = conserve ke, no = do not conserve ke
|
|
||||||
int diff_flag; // yes = simulate diffusion of central atom, no = swap only to certain types
|
|
||||||
int rates_flag; // yes = use modified type rates, no = swap rates are equivilent across types
|
|
||||||
int ncycles;
|
|
||||||
int niswap, njswap; // # of i,j swap atoms on all procs
|
|
||||||
int niswap_local, njswap_local; // # of swap atoms on this proc
|
|
||||||
int niswap_before, njswap_before; // # of swap atoms on procs < this proc
|
|
||||||
class Region *region; // swap region
|
|
||||||
char *idregion; // swap region id
|
|
||||||
|
|
||||||
int nswaptypes;
|
|
||||||
int jtype_selected;
|
|
||||||
int id_center;
|
|
||||||
double x_center;
|
|
||||||
double y_center;
|
|
||||||
double z_center;
|
|
||||||
int *type_list;
|
|
||||||
double *rate_list;
|
|
||||||
|
|
||||||
double nswap_attempts;
|
|
||||||
double nswap_successes;
|
|
||||||
|
|
||||||
bool unequal_cutoffs;
|
|
||||||
|
|
||||||
int atom_swap_nmax;
|
|
||||||
double beta, inv_r_0;
|
|
||||||
double local_probability; // Total swap probability stored on this proc
|
|
||||||
double global_probability; // Total swap probability across all proc
|
|
||||||
double prev_probability; // Swap probability on proc < this proc
|
|
||||||
double *qtype;
|
|
||||||
double energy_stored;
|
|
||||||
double **sqrt_mass_ratio;
|
|
||||||
double **voro_neighbor_list;
|
|
||||||
int *local_swap_iatom_list;
|
|
||||||
int *local_swap_neighbor_list;
|
|
||||||
int *local_swap_type_list; // Type list index of atoms stored on this proc
|
|
||||||
double *local_swap_probability;
|
|
||||||
|
|
||||||
class RanPark *random_equal;
|
|
||||||
|
|
||||||
char *id_voro;
|
|
||||||
class Compute *c_voro, *c_pe;
|
|
||||||
|
|
||||||
void options(int, char **);
|
|
||||||
int attempt_swap();
|
|
||||||
double energy_full();
|
|
||||||
int pick_i_swap_atom();
|
|
||||||
int pick_j_swap_neighbor();
|
|
||||||
void build_i_neighbor_list(int);
|
|
||||||
void update_iswap_atoms_list();
|
|
||||||
};
|
|
||||||
|
|
||||||
} // namespace LAMMPS_NS
|
|
||||||
|
|
||||||
#endif
|
|
||||||
#endif
|
|
||||||
@ -19,6 +19,8 @@
|
|||||||
#include "fmt/format.h"
|
#include "fmt/format.h"
|
||||||
#include "utils.h"
|
#include "utils.h"
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
#include <cstdlib>
|
||||||
#include <utility>
|
#include <utility>
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
@ -365,6 +367,11 @@ double ValueTokenizer::next_double()
|
|||||||
return val;
|
return val;
|
||||||
// rethrow exceptions from std::stod()
|
// rethrow exceptions from std::stod()
|
||||||
} catch (std::out_of_range const &) {
|
} catch (std::out_of_range const &) {
|
||||||
|
// could be a denormal number. try again with std::strtod().
|
||||||
|
char *end;
|
||||||
|
auto val = std::strtod(current.c_str(), &end);
|
||||||
|
// return value of denormal
|
||||||
|
if ((val > -HUGE_VAL) && (val < HUGE_VAL)) return val;
|
||||||
throw InvalidFloatException(current);
|
throw InvalidFloatException(current);
|
||||||
} catch (std::invalid_argument const &) {
|
} catch (std::invalid_argument const &) {
|
||||||
throw InvalidFloatException(current);
|
throw InvalidFloatException(current);
|
||||||
|
|||||||
@ -34,6 +34,8 @@
|
|||||||
|
|
||||||
#include <cctype>
|
#include <cctype>
|
||||||
#include <cerrno>
|
#include <cerrno>
|
||||||
|
#include <cmath>
|
||||||
|
#include <cstdlib>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
#include <ctime>
|
#include <ctime>
|
||||||
#include <stdexcept>
|
#include <stdexcept>
|
||||||
@ -272,6 +274,11 @@ void utils::print(FILE *fp, const std::string &mesg)
|
|||||||
fputs(mesg.c_str(), fp);
|
fputs(mesg.c_str(), fp);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
void utils::print(const std::string &mesg)
|
||||||
|
{
|
||||||
|
fputs(mesg.c_str(), stdout);
|
||||||
|
}
|
||||||
|
|
||||||
void utils::fmtargs_print(FILE *fp, fmt::string_view format, fmt::format_args args)
|
void utils::fmtargs_print(FILE *fp, fmt::string_view format, fmt::format_args args)
|
||||||
{
|
{
|
||||||
print(fp, fmt::vformat(format, args));
|
print(fp, fmt::vformat(format, args));
|
||||||
@ -529,7 +536,7 @@ double utils::numeric(const char *file, int line, const std::string &str, bool d
|
|||||||
lmp->error->all(file, line, msg);
|
lmp->error->all(file, line, msg);
|
||||||
}
|
}
|
||||||
|
|
||||||
double rv = 0;
|
double rv = 0.0;
|
||||||
auto msg = fmt::format("Floating point number {} in input script or data file is invalid", buf);
|
auto msg = fmt::format("Floating point number {} in input script or data file is invalid", buf);
|
||||||
try {
|
try {
|
||||||
std::size_t endpos;
|
std::size_t endpos;
|
||||||
@ -546,6 +553,12 @@ double utils::numeric(const char *file, int line, const std::string &str, bool d
|
|||||||
else
|
else
|
||||||
lmp->error->all(file, line, msg);
|
lmp->error->all(file, line, msg);
|
||||||
} catch (std::out_of_range const &) {
|
} catch (std::out_of_range const &) {
|
||||||
|
// could be a denormal number. try again with std::strtod().
|
||||||
|
char *end;
|
||||||
|
rv = std::strtod(buf.c_str(), &end);
|
||||||
|
// return value if denormal
|
||||||
|
if ((rv > -HUGE_VAL) && (rv < HUGE_VAL)) return rv;
|
||||||
|
|
||||||
msg = fmt::format("Floating point number {} in input script or data file is out of range", buf);
|
msg = fmt::format("Floating point number {} in input script or data file is out of range", buf);
|
||||||
if (do_abort)
|
if (do_abort)
|
||||||
lmp->error->one(file, line, msg);
|
lmp->error->one(file, line, msg);
|
||||||
|
|||||||
22
src/utils.h
22
src/utils.h
@ -151,7 +151,7 @@ output are compressed to a single blank by calling :cpp:func:`strcompress()`
|
|||||||
|
|
||||||
\endverbatim
|
\endverbatim
|
||||||
*
|
*
|
||||||
* This function implements a version of fprintf() that uses {fmt} formatting
|
* This function implements a version of (f)printf() that uses {fmt} formatting
|
||||||
*
|
*
|
||||||
* \param fp stdio FILE pointer
|
* \param fp stdio FILE pointer
|
||||||
* \param format format string of message to be printed
|
* \param format format string of message to be printed
|
||||||
@ -163,12 +163,32 @@ output are compressed to a single blank by calling :cpp:func:`strcompress()`
|
|||||||
}
|
}
|
||||||
|
|
||||||
/*! \overload
|
/*! \overload
|
||||||
|
*
|
||||||
|
* Print to stdout without specifying the FILE pointer.
|
||||||
|
*
|
||||||
|
* \param mesg string with message to be printed */
|
||||||
|
template <typename... Args> void print(const std::string &format, Args &&...args)
|
||||||
|
{
|
||||||
|
fmtargs_print(stdout, format, fmt::make_format_args(args...));
|
||||||
|
}
|
||||||
|
|
||||||
|
/*! \overload
|
||||||
|
*
|
||||||
|
* Print string message without format
|
||||||
*
|
*
|
||||||
* \param fp stdio FILE pointer
|
* \param fp stdio FILE pointer
|
||||||
* \param mesg string with message to be printed */
|
* \param mesg string with message to be printed */
|
||||||
|
|
||||||
void print(FILE *fp, const std::string &mesg);
|
void print(FILE *fp, const std::string &mesg);
|
||||||
|
|
||||||
|
/*! \overload
|
||||||
|
*
|
||||||
|
* Print string message without format to stdout
|
||||||
|
*
|
||||||
|
* \param mesg string with message to be printed */
|
||||||
|
|
||||||
|
void print(const std::string &mesg);
|
||||||
|
|
||||||
/*! Return text redirecting the user to a specific paragraph in the manual
|
/*! Return text redirecting the user to a specific paragraph in the manual
|
||||||
*
|
*
|
||||||
* The LAMMPS manual contains detailed explanations for errors and
|
* The LAMMPS manual contains detailed explanations for errors and
|
||||||
|
|||||||
@ -482,6 +482,7 @@ fix_aveforce.html fix aveforce
|
|||||||
fix_ave_grid.html fix ave/grid
|
fix_ave_grid.html fix ave/grid
|
||||||
fix_ave_histo.html fix ave/histo
|
fix_ave_histo.html fix ave/histo
|
||||||
fix_ave_histo.html fix ave/histo/weight
|
fix_ave_histo.html fix ave/histo/weight
|
||||||
|
fix_ave_moments.html fix ave/moments
|
||||||
fix_ave_time.html fix ave/time
|
fix_ave_time.html fix ave/time
|
||||||
fix_balance.html fix balance
|
fix_balance.html fix balance
|
||||||
fix_bocs.html fix bocs
|
fix_bocs.html fix bocs
|
||||||
@ -542,6 +543,7 @@ fix_flow_gauss.html fix flow/gauss
|
|||||||
fix_freeze.html fix freeze
|
fix_freeze.html fix freeze
|
||||||
fix_freeze.html fix freeze/kk
|
fix_freeze.html fix freeze/kk
|
||||||
fix_gcmc.html fix gcmc
|
fix_gcmc.html fix gcmc
|
||||||
|
fix_gjf.html fix gjf
|
||||||
fix_gld.html fix gld
|
fix_gld.html fix gld
|
||||||
fix_gle.html fix gle
|
fix_gle.html fix gle
|
||||||
fix_gravity.html fix gravity
|
fix_gravity.html fix gravity
|
||||||
@ -732,6 +734,7 @@ fix_saed_vtk.html fix saed/vtk
|
|||||||
fix_setforce.html fix setforce
|
fix_setforce.html fix setforce
|
||||||
fix_setforce.html fix setforce/kk
|
fix_setforce.html fix setforce/kk
|
||||||
fix_setforce.html fix setforce/spin
|
fix_setforce.html fix setforce/spin
|
||||||
|
fix_set.html fix set
|
||||||
fix_sgcmc.html fix sgcmc
|
fix_sgcmc.html fix sgcmc
|
||||||
fix_shake.html fix rattle
|
fix_shake.html fix rattle
|
||||||
fix_shake.html fix shake
|
fix_shake.html fix shake
|
||||||
|
|||||||
@ -57,7 +57,7 @@
|
|||||||
<releases>
|
<releases>
|
||||||
<release version="1.6.14" timestamp="1747828753">
|
<release version="1.6.14" timestamp="1747828753">
|
||||||
<description>
|
<description>
|
||||||
...
|
Must set en_US.UTF-8 locale on macOS since it lacks support for C.UTF-8
|
||||||
</description>
|
</description>
|
||||||
</release>
|
</release>
|
||||||
<release version="1.6.13" timestamp="1743734509">
|
<release version="1.6.13" timestamp="1743734509">
|
||||||
|
|||||||
@ -36,8 +36,13 @@ int main(int argc, char *argv[])
|
|||||||
qRegisterMetaTypeStreamOperators<QList<QString>>("QList<QString>");
|
qRegisterMetaTypeStreamOperators<QList<QString>>("QList<QString>");
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
|
#ifndef Q_OS_MACOS
|
||||||
// enforce using the plain ASCII C locale with UTF-8 encoding within the GUI.
|
// enforce using the plain ASCII C locale with UTF-8 encoding within the GUI.
|
||||||
qputenv("LC_ALL", "C.UTF-8");
|
qputenv("LC_ALL", "C.UTF-8");
|
||||||
|
#else
|
||||||
|
// macOS does not support "C" locale with UTF-8 encoding, but Qt requires UTF-8
|
||||||
|
qputenv("LC_ALL", "en_US.UTF-8");
|
||||||
|
#endif
|
||||||
|
|
||||||
QApplication app(argc, argv);
|
QApplication app(argc, argv);
|
||||||
QCoreApplication::setOrganizationName("The LAMMPS Developers");
|
QCoreApplication::setOrganizationName("The LAMMPS Developers");
|
||||||
|
|||||||
Reference in New Issue
Block a user