diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index 91851d54f3..b54e585f69 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -47,60 +47,60 @@ Description Pair style *pace* computes interactions using the Atomic Cluster Expansion (ACE), which is a general expansion of the atomic energy in -multi-body basis functions. :ref:`(Drautz) `. -The *pace* pair style -provides an efficient implementation that -is described in this paper :ref:`(Lysogorskiy) `. +multi-body basis functions. :ref:`(Drautz) `. The *pace* +pair style provides an efficient implementation that is described in +this paper :ref:`(Lysogorskiy) `. -In ACE, the total energy is decomposed into a sum over -atomic energies. The energy of atom *i* is expressed as a -linear or non-linear function of one or more density functions. -By projecting the -density onto a local atomic base, the lowest order contributions -to the energy can be expressed as a set of scalar polynomials in -basis function contributions summed over neighbor atoms. +In ACE, the total energy is decomposed into a sum over atomic +energies. The energy of atom *i* is expressed as a linear or non-linear +function of one or more density functions. By projecting the density +onto a local atomic base, the lowest order contributions to the energy +can be expressed as a set of scalar polynomials in basis function +contributions summed over neighbor atoms. Only a single pair_coeff command is used with the *pace* style which specifies an ACE coefficient file followed by N additional arguments -specifying the mapping of ACE elements to LAMMPS atom types, -where N is the number of LAMMPS atom types: +specifying the mapping of ACE elements to LAMMPS atom types, where N is +the number of LAMMPS atom types: * ACE coefficient file * N element names = mapping of ACE elements to atom types Only a single pair_coeff command is used with the *pace* style which -specifies an ACE file that fully defines the potential. -Note that unlike for other potentials, cutoffs are -not set in the pair_style or pair_coeff command; they are specified in -the ACE file. +specifies an ACE file that fully defines the potential. Note that +unlike for other potentials, cutoffs are not set in the pair_style or +pair_coeff command; they are specified in the ACE file. The pair_style *pace* command may be followed by the optional keyword -*product* or *recursive*, which determines which of two algorithms -is used for the calculation of basis functions and derivatives. -The default is *recursive*. +*product* or *recursive*, which determines which of two algorithms is +used for the calculation of basis functions and derivatives. The +default is *recursive*. -The keyword *chunksize* is only applicable when -using the pair style *pace* with the KOKKOS package on GPUs and is -ignored otherwise. This keyword controls the number of atoms -in each pass used to compute the atomic cluster expansion and is used to -avoid running out of memory. For example if there are 8192 atoms in the -simulation and the *chunksize* is set to 4096, the ACE -calculation will be broken up into two passes (running on a single GPU). +The keyword *chunksize* is only applicable when using the pair style +*pace* with the KOKKOS package on GPUs and is ignored otherwise. This +keyword controls the number of atoms in each pass used to compute the +atomic cluster expansion and is used to avoid running out of memory. +For example if there are 8192 atoms in the simulation and the +*chunksize* is set to 4096, the ACE calculation will be broken up into +two passes (running on a single GPU). Extrapolation grade """"""""""""""""""" -Calculation of extrapolation grade in PACE is implemented in `pair_style pace/extrapolation`. -It is based on the MaxVol algorithm similar to Moment Tensor Potential (MTP) by Shapeev et al. -and is described in :ref:`(Lysogorskiy2) `. -In order to compute extrapolation grade one needs to provide: +Calculation of extrapolation grade in PACE is implemented in `pair_style +pace/extrapolation`. It is based on the MaxVol algorithm similar to +Moment Tensor Potential (MTP) by Shapeev et al. and is described in +:ref:`(Lysogorskiy2) `. In order to compute +extrapolation grade one needs to provide: #. ACE potential in B-basis form (`.yaml` format) and #. Active Set Inverted (ASI) file for corresponding potential (`.asi` format) -Calculation of extrapolation grades requires matrix-vector multiplication for each atom -and is slower than the usual `pair_style pace recursive`, therefore it is *not* computed by default. -Extrapolation grade calculation is involved by `fix pair`, which requests to compute `gamma`, as shown in example below: +Calculation of extrapolation grades requires matrix-vector +multiplication for each atom and is slower than the usual `pair_style +pace recursive`, therefore it is *not* computed by default. +Extrapolation grade calculation is involved by `fix pair`, which +requests to compute `gamma`, as shown in example below: .. code-block:: LAMMPS @@ -119,10 +119,12 @@ Extrapolation grade calculation is involved by `fix pair`, which requests to com variable max_pace_gamma equal c_max_pace_gamma fix extreme_extrapolation all halt 10 v_max_pace_gamma > 25 -Here extrapolation grade gamma is computed every 10 steps and is stored in `f_pace_gamma` per-atom variable. -The largest value of extrapolation grade among all atoms in a structure is reduced to `c_max_pace_gamma` variable. -Only if this value exceeds extrapolation threshold 5, then the structure will be dumped into `extrapolative_structures.dump` -file, but not more often than every 20 steps. +Here extrapolation grade gamma is computed every 10 steps and is stored +in `f_pace_gamma` per-atom variable. The largest value of extrapolation +grade among all atoms in a structure is reduced to `c_max_pace_gamma` +variable. Only if this value exceeds extrapolation threshold 5, then +the structure will be dumped into `extrapolative_structures.dump` file, +but not more often than every 20 steps. On all other steps `pair_style pace recursive` will be used. @@ -142,9 +144,10 @@ specify a pair_coeff command with I != J arguments for this style. This pair style does not support the :doc:`pair_modify ` shift, table, and tail options. -This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. +This pair style does not write its information to :doc:`binary restart +files `, since it is stored in potential files. Thus, you need +to re-specify the pair_style and pair_coeff commands in an input script +that reads a restart file. This pair style can only be used via the *pair* keyword of the :doc:`run_style respa ` command. It does not support the @@ -159,9 +162,9 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This pair style is part of the ML-PACE package. It is only enabled if LAMMPS -was built with that package. -See the :doc:`Build package ` page for more info. +This pair style is part of the ML-PACE package. It is only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 15316b4f09..99fe278c45 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2381,6 +2381,7 @@ Nmols nn nnodes npits +npj nO Nocedal nocite @@ -3154,6 +3155,7 @@ sfree Sg Shan Shanno +Shapeev shapex shapey shapez