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Merge remote-tracking branch 'github/develop' into restricted-angle

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Axel Kohlmeyer
2024-04-13 02:45:53 -04:00
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14
doc/src/Build_extras.rst
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@ -533,9 +533,6 @@ They must be specified in uppercase.
* - A64FX
- HOST
- ARMv8.2 with SVE Support
* - WSM
- HOST
- Intel Westmere CPU (SSE 4.2)
* - SNB
- HOST
- Intel Sandy/Ivy Bridge CPU (AVX 1)
@ -566,18 +563,15 @@ They must be specified in uppercase.
* - KNL
- HOST
- Intel Knights Landing Xeon Phi
* - BGQ
- HOST
- IBM Blue Gene/Q CPU
* - POWER7
- HOST
- IBM POWER7 CPU
* - POWER8
- HOST
- IBM POWER8 CPU
* - POWER9
- HOST
- IBM POWER9 CPU
* - RISCV_SG2042
- HOST
- SG2042 (RISC-V) CPU
* - KEPLER30
- GPU
- NVIDIA Kepler generation CC 3.0 GPU
@ -666,7 +660,7 @@ They must be specified in uppercase.
- GPU
- Intel GPU Ponte Vecchio
This list was last updated for version 4.2 of the Kokkos library.
This list was last updated for version 4.3.0 of the Kokkos library.
.. tabs::

1
doc/src/Commands_pair.rst
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@ -245,6 +245,7 @@ OPT.
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`pace (k) <pair_pace>`
* :doc:`pace/extrapolation (k) <pair_pace>`
* :doc:`pedone (o) <pair_pedone>`
* :doc:`pod <pair_pod>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`

4
doc/src/Developer_utils.rst
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@ -635,10 +635,10 @@ Tohoku University (under MIT license)
----------
.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec)
.. doxygenfunction:: MathEigen::jacobi3(double const *const *mat, double *eval, double **evec, int sort)
:project: progguide
.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3])
.. doxygenfunction:: MathEigen::jacobi3(double const mat[3][3], double *eval, double evec[3][3], int sort)
:project: progguide
---------------------------

49
doc/src/Errors_details.rst
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@ -13,15 +13,44 @@ discussions of such cases.
Unknown identifier in data file
-------------------------------
This error happens when LAMMPS encounters a line of text in an unexpected format
while reading a data file. This is most commonly cause by inconsistent header and
section data. The header section informs LAMMPS how many entries or lines are expected in the
various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of the data file.
If there is a mismatch, LAMMPS will either keep reading beyond the end of a section
or stop reading before the section has ended.
This error happens when LAMMPS encounters a line of text with an
unexpected keyword while :doc:`reading a data file <read_data>`. This
would be either header keywords or section header keywords. This is
most commonly due to a mistyped keyword or due to a keyword that is
inconsistent with the :doc:`atom style <atom_style>` used.
Such a mismatch can happen unexpectedly when the first line of the data
is *not* a comment as required by the format. That would result in
LAMMPS expecting, for instance, 0 atoms because the "atoms" header line
is treated as a comment.
The header section informs LAMMPS how many entries or lines are expected
in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of
the data file. If there is a mismatch, LAMMPS will either keep reading
beyond the end of a section or stop reading before the section has
ended. In that case the next line will not contain a recognized keyword.
Such a mismatch can also happen when the first line of the data
is *not* a comment as required by the format, but a line with a valid
header keyword. That would result in LAMMPS expecting, for instance,
0 atoms because the "atoms" header line is the first line and thus
treated as a comment.
Another possibility to trigger this error is to have a keyword in the
data file that corresponds to a fix (e.g. :doc:`fix cmap <fix_cmap>`)
but the :doc:`read_data <read_data>` command is missing the (optional)
arguments that identify the fix and the header keyword and section
keyword or those arguments are inconsistent with the keywords in the
data file.
.. _err0002:
Incorrect format in ... section of data file
--------------------------------------------
This error happens when LAMMPS reads the contents of a section of a
:doc:`data file <read_data>` and the number of parameters in the line
differs from what is expected. This most commonly happens, when the
atom style is different from what is expected for a specific data file
since changing the atom style usually changes the format of the line.
This error can also happen when the number of entries indicated in the
header of a data file (e.g. the number of atoms) is larger than the
number of lines provided (e.g. in the corresponding Atoms section)
and then LAMMPS will continue reading into the next section and that
would have a completely different format.

1
doc/src/fix_ave_correlate.rst
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@ -65,7 +65,6 @@ Examples
fix 1 all ave/correlate 1 50 10000 &
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
type upper ave running title1 "My correlation data"
fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]
Description

13
doc/src/fix_ave_correlate_long.rst
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@ -20,11 +20,11 @@ Syntax
.. parsed-literal::
c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
v_name = global value calculated by an equal-style variable with name
v_name[I] = Ith component of global vector calculated by a vector-style variable with name
v_name[I] = Ith component of a vector-style variable with name, I can include wildcard (see below)
* zero or more keyword/arg pairs may be appended
* keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount*
@ -63,6 +63,7 @@ Examples
fix 1 all ave/correlate/long 1 10000 &
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
type upper title1 "My correlation data" nlen 15 ncount 3
fix 1 all ave/correlate/long 1 10000 c_thermo_press[*]
Description
"""""""""""
@ -80,8 +81,10 @@ specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each listed value can be the result of a compute or fix or the
evaluation of an equal-style variable. See the
:doc:`fix ave/correlate <fix_ave_correlate>` page for details.
evaluation of an equal-style or vector-style variable. For
vector-style variables, the specified indices can include a wildcard
character. See the :doc:`fix ave/correlate <fix_ave_correlate>` page
for details.
The *Nevery* and *Nfreq* arguments specify on what time steps the input
values will be used to calculate correlation data and the frequency

75
doc/src/fix_ttm.rst
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@ -136,23 +136,23 @@ transfer between the subsystems:
\bigtriangledown (\kappa_e \bigtriangledown T_e) -
g_p (T_e - T_a) + g_s T_a'
where C_e is the specific heat, rho_e is the density, kappa_e is the
thermal conductivity, T is temperature, the "e" and "a" subscripts
represent electronic and atomic subsystems respectively, g_p is the
coupling constant for the electron-ion interaction, and g_s is the
electron stopping coupling parameter. C_e, rho_e, and kappa_e are
specified as parameters to the fix. The other quantities are derived.
The form of the heat diffusion equation used here is almost the same
as that in equation 6 of :ref:`(Duffy) <Duffy>`, with the exception that the
electronic density is explicitly represented, rather than being part
of the specific heat parameter.
where :math:`C_e` is the specific heat, :math:`\rho_e` is the density,
:math:`\kappa_e` is the thermal conductivity, *T* is temperature, the
"e" and "a" subscripts represent electronic and atomic subsystems
respectively, :math:`g_p` is the coupling constant for the electron-ion
interaction, and :math:`g_s` is the electron stopping coupling
parameter. :math:`C_e`, :math:`\rho_e`, and :math:`\kappa_e` are
specified as parameters to the fix *ttm* or *ttm/grid*. The other
quantities are derived. The form of the heat diffusion equation used
here is almost the same as that in equation 6 of :ref:`(Duffy) <Duffy>`,
with the exception that the electronic density is explicitly
represented, rather than being part of the specific heat parameter.
Currently, the TTM fixes assume that none of the user-supplied
parameters will vary with temperature. Note that :ref:`(Duffy)
<Duffy>` used a tanh() functional form for the temperature dependence
of the electronic specific heat, but ignored temperature dependencies
of any of the other parameters. See more discussion below for fix
ttm/mod.
parameters will vary with temperature. Note that :ref:`(Duffy) <Duffy>`
used a tanh() functional form for the temperature dependence of the
electronic specific heat, but ignored temperature dependencies of any of
the other parameters. See more discussion below for fix *ttm/mod*.
.. note::
@ -265,27 +265,27 @@ heat sources (e.g. laser heating in ablation simulations):
\bigtriangledown (\kappa_e \bigtriangledown T_e) -
g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin})
where theta is the Heaviside step function, I_0 is the (absorbed)
laser pulse intensity for ablation simulations, l_skin is the depth
of skin-layer, and all other designations have the same meaning as in
the former equation. The duration of the pulse is set by the parameter
*tau* in the *init_file*.
where :math:`\theta` is the Heaviside step function, :math:`I_0` is the
(absorbed) laser pulse intensity for ablation simulations,
:math:`l_{skin}` is the depth of the skin-layer, and all other
designations have the same meaning as in the former equation. The
duration of the pulse is set by the parameter *tau* in the *init_file*.
Fix ttm/mod also allows users to specify the dependencies of C_e and
kappa_e on the electronic temperature. The specific heat is expressed
as
Fix *ttm/mod* also allows users to specify the dependencies of
:math:`C_e` and :math:`\kappa_e` on the electronic temperature. The
specific heat is expressed as
.. math::
C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2)
where *X* = T_e/1000, and the thermal conductivity is defined as
kappa_e = D_e\*rho_e\*C_e, where D_e is the thermal diffusion
coefficient.
where :math:`X = \frac{T_e}{1000}`, and the thermal conductivity is
defined as :math:`\kappa_e = D_e \cdot rho_e \cdot C_e`, where
:math:`D_e` is the thermal diffusion coefficient.
Electronic pressure effects are included in the TTM model to account
for the blast force acting on ions because of electronic pressure
gradient (see :ref:`(Chen) <Chen>`, :ref:`(Norman) <Norman>`). The total force
Electronic pressure effects are included in the TTM model to account for
the blast force acting on ions because of electronic pressure gradient
(see :ref:`(Chen) <Chen>`, :ref:`(Norman) <Norman>`). The total force
acting on an ion is:
.. math::
@ -293,13 +293,14 @@ acting on an ion is:
{\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec
F}_{langevin} - \nabla P_e/n_{ion}
where F_langevin is a force from Langevin thermostat simulating
electron-phonon coupling, and nabla P_e/n_ion is the electron blast
force.
where :math:`F_{langevin}` is a force from Langevin thermostat
simulating electron-phonon coupling, and :math:`\nabla P_e/n_{ion}` is
the electron blast force.
The electronic pressure is taken to be P_e = B\*rho_e\*C_e\*T_e
The electronic pressure is taken to be :math:`P_e = B \cdot rho_e \cdot
C_e \cdot T_e`
The current fix ttm/mod implementation allows TTM simulations with a
The current fix *ttm/mod* implementation allows TTM simulations with a
vacuum. The vacuum region is defined as the grid cells with zero
electronic temperature. The numerical scheme does not allow energy
exchange with such cells. Since the material can expand to previously
@ -319,10 +320,10 @@ electronic pressure gradient is calculated as
\frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta
x}-(C_e{}T_e)_{x}}{\Delta x} \right]
where lambda is the electron mean free path (see :ref:`(Norman) <Norman>`,
:ref:`(Pisarev) <Pisarev>`)
where :math:`\lambda` is the electron mean free path (see :ref:`(Norman)
<Norman>`, :ref:`(Pisarev) <Pisarev>`)
The fix ttm/mod parameter file *init_file* has the following syntax.
The fix *ttm/mod* parameter file *init_file* has the following syntax.
Every line with an odd number is considered as a comment and
ignored. The lines with the even numbers are treated as follows:

137
doc/src/pair_pedone.rst Normal file
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@ -0,0 +1,137 @@
.. index:: pair_style pedone
.. index:: pair_style pedone/omp
pair_style pedone command
=========================
Accelerator Variants: *pedone/omp*
Syntax
""""""
.. code-block:: LAMMPS
pair_style style args
* style = pedone*
* args = list of arguments for a particular style
.. parsed-literal::
*pedone* args = cutoff
cutoff = global cutoff for Pedone interactions (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style hybrid/overlay pedone 15.0 coul/long 15.0
kspace_style pppm 1.0e-5
pair_coeff * * coul/long
pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0
pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0
Used in input scripts:
.. parsed-literal::
examples/PACKAGES/pedone/in.pedone.relax
examples/PACKAGES/pedone/in.pedone.melt
Description
"""""""""""
.. versionadded:: TBD
Pair style *pedone* computes the **non-Coulomb** interactions of the Pedone
(or PMMCS) potential :ref:`(Pedone) <Pedone>` which combines Coulomb
interactions, Morse potential, and repulsive :math:`r^{-12}`
Lennard-Jones terms (see below). The *pedone* pair style is meant
to be used in addition to a :doc:`Coulomb pair style <pair_coul>` via
pair style :doc:`hybrid/overlay <pair_hybrid>` (see example above).
Using *coul/long* or *could/dsf* (for solids) is recommended.
The full Pedone potential function from :ref:`(Pedone) <Pedone>` for each
pair of atoms is:
.. math::
E = \frac{C q_i q_j}{\epsilon r}
+ D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
+ \frac{B_0}{r^{12}} \qquad r < r_c
:math:`r_c` is the cutoff and :math:`C` is a conversion factor that is
specific to the choice of :doc:`units <units>` so that the entire
Coulomb term is in energy units with :math:`q_i` and :math:`q_j` as the
assigned charges in multiples of the elementary charge.
The following coefficients must be defined for the selected pairs of
atom types via the :doc:`pair_coeff <pair_coeff>` command as in the
example above:
* :math:`D_0` (energy units)
* :math:`\alpha` (1/distance units)
* :math:`r_0` (distance units)
* :math:`C_0` (energy units)
* cutoff (distance units)
The last coefficient is optional. If not specified, the global *pedone*
cutoff is used.
----------
.. include:: accel_styles.rst
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This pair style does not support mixing.
This pair style support the :doc:`pair_modify <pair_modify>` shift
option for the energy of the pair interaction.
This pair style does not support the :doc:`pair_modify <pair_modify>`
tail option for adding long-range tail corrections to energy and
pressure.
This pair style writes its information to :doc:`binary restart files <restart>`,
so pair_style and pair_coeff commands does not need to be specified 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 <run_style>` command. It does not support the
*inner*, *middle*, or *outer* keywords.
----------
Restrictions
""""""""""""
The *pedone* pair style is only enabled if LAMMPS was built with the
EXTRA-PAIR package. See the :doc:`Build package <Build_package>` page
for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style <pair_style>`,
:doc:`pair style coul/long and coul/dsf <pair_coul>`,
:doc:`pair style morse <pair_morse>`
Default
"""""""
none
-------------
.. _Pedone:
**(Pedone)** A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006)

49
doc/src/pair_style.rst
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@ -275,30 +275,30 @@ accelerated styles exist.
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed LJ vdW potential with Gaussian electrostatics
* :doc:`lj96/cut <pair_lj96>` - Lennard-Jones 9/6 potential
* :doc:`local/density <pair_local_density>` - generalized basic local density potential
* :doc:`lubricate <pair_lubricate>` - hydrodynamic lubrication forces
* :doc:`lubricate/poly <pair_lubricate>` - hydrodynamic lubrication forces with polydispersity
* :doc:`lubricateU <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication Dynamics
* :doc:`lubricateU/poly <pair_lubricateU>` - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
* :doc:`local/density <pair_local_density>` - Generalized basic local density potential
* :doc:`lubricate <pair_lubricate>` - Hydrodynamic lubrication forces
* :doc:`lubricate/poly <pair_lubricate>` - Hydrodynamic lubrication forces with polydispersity
* :doc:`lubricateU <pair_lubricateU>` - Hydrodynamic lubrication forces for Fast Lubrication Dynamics
* :doc:`lubricateU/poly <pair_lubricateU>` - Hydrodynamic lubrication forces for Fast Lubrication with polydispersity
* :doc:`mdpd <pair_mesodpd>` - mDPD particle interactions
* :doc:`mdpd/rhosum <pair_mesodpd>` - mDPD particle interactions for mass density
* :doc:`meam <pair_meam>` - modified embedded atom method (MEAM)
* :doc:`meam/ms <pair_meam>` - multi-state modified embedded atom method (MS-MEAM)
* :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
* :doc:`mesocnt <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes
* :doc:`mesocnt/viscous <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes with friction
* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
* :doc:`meam <pair_meam>` - Modified embedded atom method (MEAM)
* :doc:`meam/ms <pair_meam>` - Multi-state modified embedded atom method (MS-MEAM)
* :doc:`meam/spline <pair_meam_spline>` - Splined version of MEAM
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - Splined version of MEAM with a Stillinger-Weber term
* :doc:`mesocnt <pair_mesocnt>` - Mesoscopic vdW potential for (carbon) nanotubes
* :doc:`mesocnt/viscous <pair_mesocnt>` - Mesoscopic vdW potential for (carbon) nanotubes with friction
* :doc:`mgpt <pair_mgpt>` - Simplified model generalized pseudopotential theory (MGPT) potential
* :doc:`mie/cut <pair_mie>` - Mie potential
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - Smoothed MM3 vdW potential with Gaussian electrostatics
* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
* :doc:`morse <pair_morse>` - Morse potential
* :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential
* :doc:`morse/smooth/linear <pair_morse>` - Linear smoothed Morse potential
* :doc:`morse/soft <pair_morse>` - Morse potential with a soft core
* :doc:`multi/lucy <pair_multi_lucy>` - DPD potential with density-dependent force
* :doc:`multi/lucy/rx <pair_multi_lucy_rx>` - reactive DPD potential with density-dependent force
* :doc:`nb3b/harmonic <pair_nb3b>` - non-bonded 3-body harmonic potential
* :doc:`nb3b/screened <pair_nb3b>` - non-bonded 3-body screened harmonic potential
* :doc:`nb3b/harmonic <pair_nb3b>` - Non-bonded 3-body harmonic potential
* :doc:`nb3b/screened <pair_nb3b>` - Non-bonded 3-body screened harmonic potential
* :doc:`nm/cut <pair_nm>` - N-M potential
* :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb
* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulomb
@ -322,21 +322,22 @@ accelerated styles exist.
* :doc:`oxrna2/xstk <pair_oxrna2>` -
* :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
* :doc:`pace/extrapolation <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades
* :doc:`pedone <pair_pedone>` - Pedone (PMMCS) potential (non-Coulomb part)
* :doc:`pod <pair_pod>` - Proper orthogonal decomposition (POD) machine-learning potential
* :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
* :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
* :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
* :doc:`peri/ves <pair_peri>` - peridynamic VES potential
* :doc:`polymorphic <pair_polymorphic>` - polymorphic 3-body potential
* :doc:`peri/eps <pair_peri>` - Peridynamic EPS potential
* :doc:`peri/lps <pair_peri>` - Peridynamic LPS potential
* :doc:`peri/pmb <pair_peri>` - Peridynamic PMB potential
* :doc:`peri/ves <pair_peri>` - Peridynamic VES potential
* :doc:`polymorphic <pair_polymorphic>` - Polymorphic 3-body potential
* :doc:`python <pair_python>` -
* :doc:`quip <pair_quip>` -
* :doc:`rann <pair_rann>` -
* :doc:`reaxff <pair_reaxff>` - ReaxFF potential
* :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
* :doc:`rebo <pair_airebo>` - Second generation REBO potential of Brenner
* :doc:`rebomos <pair_rebomos>` - REBOMoS potential for MoS2
* :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
* :doc:`saip/metal <pair_saip_metal>` - interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
* :doc:`saip/metal <pair_saip_metal>` - Interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - Smoothed dissipative particle dynamics for water at isothermal conditions
* :doc:`smatb <pair_smatb>` - Second Moment Approximation to the Tight Binding
* :doc:`smatb/single <pair_smatb>` - Second Moment Approximation to the Tight Binding for single-element systems
* :doc:`smd/hertz <pair_smd_hertz>` -

79
doc/src/variable.rst
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@ -279,9 +279,9 @@ This means the variable can then be evaluated as many times as desired
and will return those values. There are two ways to cause the next
set of per-atom values from the file to be read: use the
:doc:`next <next>` command or the next() function in an atom-style
variable, as discussed below. Unlike most variable styles
atomfile-style variables are **deleted** during a :doc:`clear <clear>`
command.
variable, as discussed below. Unlike most variable styles, which
remain defined, atomfile-style variables are **deleted** during a
:doc:`clear <clear>` command.
The rules for formatting the file are as follows. Each time a set of
per-atom values is read, a non-blank line is searched for in the file.
@ -289,23 +289,37 @@ The file is read line by line but only up to 254 characters are used.
The rest are ignored. A comment character "#" can be used anywhere
on a line and all text following and the "#" character are ignored;
text starting with the comment character is stripped. Blank lines
are skipped. The first "word" of a non-blank line, delimited by
white-space, is read as the count N of per-atom lines to immediately
follow. N can be the total number of atoms in the system, or only a
subset. The next N lines have the following format
.. parsed-literal::
ID value
where ID is an atom ID and value is the per-atom numeric value that
will be assigned to that atom. IDs can be listed in any order.
are skipped. The first non-blank line is expected to contain a single
integer number as the count *N* of per-atom lines to follow. *N* can
be the total number of atoms in the system or less, indicating that data
for a subset is read. The next N lines must consist of two numbers,
the atom-ID of the atom for which a value is set followed by a floating
point number with the value. The atom-IDs may be listed in any order.
.. note::
Every time a set of per-atom lines is read, the value for all
atoms is first set to 0.0. Thus values for atoms whose ID does not
appear in the set, will remain 0.0.
Every time a set of per-atom lines is read, the value of the atomfile
variable for **all** atoms is first initialized to 0.0. Thus values
for atoms whose ID do not appear in the set in the file will remain
at 0.0.
Below is a small example for the atomfile variable file format:
.. parsed-literal::
# first set
4
# atom-ID value
3 1
4 -4
1 0.5
2 -0.5
# second set
2
2 1.0
4 -1.0
----------
@ -1174,12 +1188,17 @@ custom atom properties are the same; just replace the leading "i" with
+--------+---------------+------------------------------------------+
| equal | i_name[I] | element of per-atom vector (I = atom ID) |
+--------+---------------+------------------------------------------+
| equal | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
+--------+---------------+------------------------------------------+
| vector | i_name[I] | element of per-atom vector (I = atom ID) |
+--------+---------------+------------------------------------------+
| vector | i2_name[I][J] | element of per-atom array (I = atom ID) |
+--------+---------------+------------------------------------------+
+--------+---------------+------------------------------------------+
| atom | i_name | per-atom vector |
+--------+---------------+------------------------------------------+
| atom | i2_name[I] | column of per-atom array |
+--------+---------------+------------------------------------------+
@ -1222,15 +1241,23 @@ table:
+--------+------------+------------------------------------------+
| equal | c_ID | global scalar |
+--------+------------+------------------------------------------+
| equal | c_ID[I] | element of global vector |
+--------+------------+------------------------------------------+
| equal | c_ID[I][J] | element of global array |
+--------+------------+------------------------------------------+
| equal | C_ID[I] | element of per-atom vector (I = atom ID) |
+--------+------------+------------------------------------------+
| equal | C_ID[I][J] | element of per-atom array (I = atom ID) |
+--------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| vector | c_ID | global vector |
+--------+------------+------------------------------------------+
| vector | c_ID[I] | column of global array |
+--------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| atom | c_ID | per-atom vector |
+--------+------------+------------------------------------------+
| atom | c_ID[I] | column of per-atom array |
+--------+------------+------------------------------------------+
@ -1286,15 +1313,23 @@ and atom-style variables are listed in the following table:
+--------+------------+------------------------------------------+
| equal | f_ID | global scalar |
+--------+------------+------------------------------------------+
| equal | f_ID[I] | element of global vector |
+--------+------------+------------------------------------------+
| equal | f_ID[I][J] | element of global array |
+--------+------------+------------------------------------------+
| equal | F_ID[I] | element of per-atom vector (I = atom ID) |
+--------+------------+------------------------------------------+
| equal | F_ID[I][J] | element of per-atom array (I = atom ID) |
+--------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| vector | f_ID | global vector |
+--------+------------+------------------------------------------+
| vector | f_ID[I] | column of global array |
+--------+------------+------------------------------------------+
+--------+------------+------------------------------------------+
| atom | f_ID | per-atom vector |
+--------+------------+------------------------------------------+
| atom | f_ID[I] | column of per-atom array |
+--------+------------+------------------------------------------+
@ -1365,17 +1400,27 @@ per-atom vector.
+--------+-----------+-----------------------------------------------------------------------------------+
| equal | v_name | global scalar from an equal-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| equal | v_name[I] | element of global vector from a vector-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| equal | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
+--------+-----------+-----------------------------------------------------------------------------------+
| vector | v_name | global scalar from an equal-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| vector | v_name | global vector from a vector-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| vector | v_name[I] | element of global vector from a vector-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| vector | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
+--------+-----------+-----------------------------------------------------------------------------------+
| atom | v_name | global scalar from an equal-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| atom | v_name | per-atom vector from an atom-style or atomfile-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| atom | v_name[I] | element of global vector from a vector-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+
| atom | v_name[I] | element of per-atom vector (I = atom ID) from an atom- or atomfile-style variable |
+--------+-----------+-----------------------------------------------------------------------------------+