diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index c5782f5e04..21a84a2518 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -34,6 +34,7 @@ OPT. * * * + * :doc:`3b/table ` * :doc:`adp (ko) ` * :doc:`agni (o) ` * :doc:`airebo (io) ` @@ -269,6 +270,7 @@ OPT. * :doc:`spin/neel ` * :doc:`srp ` * :doc:`sw (giko) ` + * :doc:`sw/3b/table ` * :doc:`sw/mod (o) ` * :doc:`table (gko) ` * :doc:`table/rx (k) ` diff --git a/doc/src/pair_3b_table.rst b/doc/src/pair_3b_table.rst index ae5e6c2a50..0a239883e4 100644 --- a/doc/src/pair_3b_table.rst +++ b/doc/src/pair_3b_table.rst @@ -1,4 +1,4 @@ -.. index:: pair_style 3b_table +.. index:: pair_style 3b/table pair_style 3b/table command =========================== @@ -26,22 +26,22 @@ Examples Description """"""""""" -The *3b/table* style is a pair style for generic tabulated three-body interactions. -It has been developed for (coarse-grained) simulations (of water) -with Kernel-based machine learning (ML) potentials (:ref:`Scherer2 `). -As for the pair style :doc:`pair_style sw ` -or :doc:`pair_style sw/table `, the energy of a system -is computed as a sum over three-body terms: +The *3b/table* style is a pair style for generic tabulated three-body +interactions. It has been developed for (coarse-grained) simulations +(of water) with Kernel-based machine learning (ML) potentials +(:ref:`Scherer2 `). As for the pair style :doc:`pair_style sw +` or :doc:`pair_style sw/3b/table `, the energy of +a system is computed as a sum over three-body terms: .. math:: E = \sum_i \sum_{j \neq i} \sum_{k > j} \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) -The summations in the formula are over all neighbors J -and K of atom I within a cutoff distance :math:`cut`. -In contrast to the Stillinger-Weber potential, all forces are not calculated analytically, but -read in from a three-body force/energy table which can be generated with -the csg_ml app of VOTCA as available at: . +The summations in the formula are over all neighbors J and K of atom I +within a cutoff distance :math:`cut`. In contrast to the +Stillinger-Weber potential, all forces are not calculated analytically, +but read in from a three-body force/energy table which can be generated +with the csg_ml app of VOTCA as available at: https://gitlab.mpcdf.mpg.de/votca/votca. Only a single pair_coeff command is used with the *3b/table* style which specifies a three-body potential (".3b") file with parameters for all @@ -102,14 +102,14 @@ If element 2 and element 3 are of the same type (e.g. SiCC), the distance due to the symmetry of the triplet. If element 2 and element 3 are not of the same type (e.g. SiCSi), there is no additional symmetry and the distance :math:`r_{ik}` is also varied from rmin to rmax in "N" steps. -The angle :math:`\theta_{ijk}` is alsways varied in "2N" steps from +The angle :math:`\theta_{ijk}` is always varied in "2N" steps from (0.0 + 180.0/(4N)) to (180.0 - 180.0/(4N)). Therefore, the total number of table entries is "M = N * N * (N+1)" for the symmetric (element 2 and element 3 are of the same type) and "M = 2 * N * N * N" for the general case (element 2 and element 3 are not of the same type). The forces on all three particles I, J, and K of a triplet -of this type of thre-body interaction potential +of this type of three-body interaction potential (:math:`\phi_3 (r_{ij}, r_{ik}, \theta_{ijk})`) lie within the plane defined by the three inter-particle distance vectors :math:`{\mathbf r}_{ij}`, :math:`{\mathbf r}_{ik}`, and :math:`{\mathbf r}_{jk}`. @@ -187,13 +187,13 @@ one that matches the specified *keyword* of appropriate section of the ".3b" fil At the moment, only the *style* *linear* is allowed and implemented. After reading in the force table, it is internally stored in LAMMPS as a lookup table. For each triplet -configuration occuring in the simulation within the cutoff distance, +configuration occurring in the simulation within the cutoff distance, the next nearest tabulated triplet configuration is looked up. No interpolation is done. This allows for a very efficient force calculation with the stored force constants and energies. Due to the know table structure, the lookup can be done efficiently. It has been tested (:ref:`Scherer2 `) that with a reasonably small bin size, the accuracy and speed is comparable to that of a Stillinger-Weber potential -with tabulated three-body interactions (:doc:`pair_style sw/table `) while +with tabulated three-body interactions (:doc:`pair_style sw/table `) while the table format of this pair style allows for more flexible three-body interactions. As for the Stillinger-Weber potential, the three-body potential file must contain entries for all the @@ -254,12 +254,12 @@ in the tutorial folder. Related commands """""""""""""""" -:doc:`pair_coeff ` +:doc:`pair_coeff `, :doc:`pair sw/3b/table ` ---------- .. _Scherer2: -**(Scherer2)** C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194–3204 (2020). +**(Scherer2)** C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194-3204 (2020). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 2bcd66590d..d24596e2fa 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -112,6 +112,7 @@ accelerated styles exist. * :doc:`hybrid/scaled ` - multiple styles of scaled superposed pairwise interactions * :doc:`zero ` - neighbor list but no interactions +* :doc:`3b/table ` - generic tabulated three-body potential * :doc:`adp ` - angular dependent potential (ADP) of Mishin * :doc:`agni ` - AGNI machine-learning potential * :doc:`airebo ` - AIREBO potential of Stuart @@ -348,6 +349,7 @@ accelerated styles exist. * :doc:`spin/neel ` - * :doc:`srp ` - * :doc:`sw ` - Stillinger-Weber 3-body potential +* :doc:`sw/3b/table ` - Stillinger-Weber potential with tabulated 3-body term * :doc:`sw/mod ` - modified Stillinger-Weber 3-body potential * :doc:`table ` - tabulated pair potential * :doc:`table/rx ` - diff --git a/doc/src/pair_sw_3b_table.rst b/doc/src/pair_sw_3b_table.rst index 97fcb63e34..2d57803a61 100644 --- a/doc/src/pair_sw_3b_table.rst +++ b/doc/src/pair_sw_3b_table.rst @@ -1,4 +1,4 @@ -.. index:: pair_style sw_3b_table +.. index:: pair_style sw/3b/table pair_style sw/3b/table command ============================== @@ -26,10 +26,12 @@ Examples Description """"""""""" -The *sw/3b/table* style is a modification of the original :doc:`pair_style sw `. It has been -developed for coarse-grained simulations (of water) (:ref:`Scherer1 `), -but can be employed for all kinds of systems. It computes a modified 3-body :ref:`Stillinger-Weber ` -potential for the energy E of a system of atoms as +The *sw/3b/table* style is a modification of the original +:doc:`pair_style sw `. It has been developed for coarse-grained +simulations (of water) (:ref:`Scherer1 `), but can be employed +for all kinds of systems. It computes a modified 3-body +:ref:`Stillinger-Weber ` potential for the energy E of a +system of atoms as .. math:: @@ -48,8 +50,8 @@ three-body term. The summations in the formula are over all neighbors J and K of atom I within a cutoff distance :math:`a \sigma`. In contrast to the original *sw* style, *sw/3b/table* allows for a flexible three-body term :math:`f^{\textrm{3b}}\left(\theta_{ijk}\right)` which is read in -as a tabulated interaction. It can be parametrized with the csg_fmatch app of VOTCA -as available at: . +as a tabulated interaction. It can be parameterized with the csg_fmatch app of VOTCA +as available at: https://gitlab.mpcdf.mpg.de/votca/votca. Only a single pair_coeff command is used with the *sw/3b/table* style which specifies a modified Stillinger-Weber potential file with parameters for all @@ -191,19 +193,21 @@ are estimated (less accurately) by the first two and last two derivative values in the table. The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium angle value, which is used, for example, by the :doc:`fix shake ` command. If not used, the equilibrium angle is -set to 180.0. +equilibrium angle value, which is used, for example, by the :doc:`fix +shake ` command. If not used, the equilibrium angle is set to +180.0. -Following a blank line, the next N lines of the angular table file list the tabulated values. -On each line, the first value is the index from 1 to N, the second value is -the angle value (in degrees), the third value is the energy (in energy -units), and the fourth is -dE/d(theta) (also in energy units). The third -term is the energy of the 3-atom configuration for the specified -angle. The last term is the derivative of the energy with respect to -the angle (in degrees, not radians). Thus the units of the last term -are still energy, not force. The angle values must increase from one -line to the next. The angle values must also begin with 0.0 and end -with 180.0, i.e. span the full range of possible angles. +Following a blank line, the next N lines of the angular table file list +the tabulated values. On each line, the first value is the index from 1 +to N, the second value is the angle value (in degrees), the third value +is the energy (in energy units), and the fourth is -dE/d(theta) (also in +energy units). The third term is the energy of the 3-atom configuration +for the specified angle. The last term is the derivative of the energy +with respect to the angle (in degrees, not radians). Thus the units of +the last term are still energy, not force. The angle values must +increase from one line to the next. The angle values must also begin +with 0.0 and end with 180.0, i.e. span the full range of possible +angles. Note that one angular potential file can contain many sections, each with a tabulated potential. LAMMPS reads the file section by section until it finds @@ -282,8 +286,8 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" -This is a user pair style. For more information, see :ref:`Scherer1 `. It is only enabled -if LAMMPS was explicitly built with it. +This is a user pair style. For more information, see :ref:`Scherer1 +`. It is only enabled if LAMMPS was explicitly built with it. This pair style requires the :doc:`newton ` setting to be "on" for pair interactions. @@ -294,12 +298,12 @@ in the tutorial folder. Related commands """""""""""""""" -:doc:`pair_coeff ` +:doc:`pair_coeff `, :doc:`pair_style sw `, :doc:`pair_style 3b/table ` ---------- -.. _Stillinger2: +.. _Stillinger3: **(Stillinger)** Stillinger and Weber, Phys Rev B, 31, 5262 (1985). diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index c8450c570b..083d25bd2f 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -94,6 +94,7 @@ amu Amzallag analytical Anders +Andrienko Andzelm Ang anglegrad @@ -239,6 +240,7 @@ benchmarking Bennet Berardi Beraun +Bereau berendsen Berendsen berger @@ -560,6 +562,7 @@ Crozier Cryst Crystallogr Csanyi +csg csh cshrc CSiC @@ -873,6 +876,7 @@ Eindhoven Eisenforschung Ejtehadi El +el elaplong elastance Electroneg @@ -1081,6 +1085,7 @@ fm fmackay fmag fmass +fmatch fmm fmt fmtlib @@ -2405,6 +2410,7 @@ Nstep Nsteplast Nstop nsub +Nsw Nswap nt Nt @@ -3034,6 +3040,7 @@ scalexz scaleyz Scalfi Schaik +Scheid Schilfgarde Schimansky Schiotz