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update docs, fix references, correct spelling issues

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Axel Kohlmeyer 2022-12-14 10:21:10 -05:00
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2
doc/src/fix.rst
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@ -360,7 +360,7 @@ accelerated styles exist.
* :doc:`saed/vtk <fix_saed_vtk>` - time-average the intensities from :doc:`compute saed <compute_saed>`
* :doc:`setforce <fix_setforce>` - set the force on each atom
* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
* :doc:`sgcmc <fix_sgcmc>` - fix for hybrid semi-grandcanonical MD/MC simulations
* :doc:`sgcmc <fix_sgcmc>` - fix for hybrid semi-grand canonical MD/MC simulations
* :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
* :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting
* :doc:`smd <fix_smd>` - applied a steered MD force to a group

83
doc/src/fix_sgcmc.rst
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@ -48,11 +48,11 @@ Description
This command allows to carry out parallel hybrid molecular
dynamics/Monte Carlo (MD/MC) simulations using the algorithms described
in [SadErhStu12]_. Simulations can be carried out in either the
semi-grandcanonical (SGC) or variance constrained semi-grandcanonical
(VC-SGC) ensemble [SadErh12]_. Only atom type swaps are performed by the
SGCMC fix. Relaxations are accounted for by the molecular dynamics
integration steps.
in :ref:`(Sadigh1) <Sadigh1>`. Simulations can be carried out in either
the semi-grand canonical (SGC) or variance constrained semi-grand
canonical (VC-SGC) ensemble :ref:`(Sadigh2) <Sadigh2>`. Only atom type
swaps are performed by the SGCMC fix. Relaxations are accounted for by
the molecular dynamics integration steps.
This fix can be used with standard multi-element EAM potentials
(:doc:`pair styles eam/alloy or eam/fs <pair_eam>`)
@ -90,26 +90,26 @@ the simulation, e.g., to speed up equilibration at low temperatures.
------------
The parameter *deltamu* is used to set the chemical potential
difference in the SGC MC algorithm (see Eq. 16 in [SadErhStu12]_). By convention
it is the difference of the chemical potentials of elements `B`, `C`
..., with respect to element A. When the simulation includes `N`
elements, `N-1` values must be specified.
The parameter *deltamu* is used to set the chemical potential difference
in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 <Sadigh1>`). By
convention it is the difference of the chemical potentials of elements
`B`, `C` ..., with respect to element A. When the simulation includes
`N` elements, `N-1` values must be specified.
------------
The variance-constrained SGC MC algorithm is activated if the keyword
*variance* is used. In that case the fix parameter *deltamu*
determines the effective average constraint in the parallel VC-SGC MC
algorithm (parameter :math:`\delta\mu_0` in Eq. (20) of [SadErhStu12]_). The
parameter *kappa* specifies the variance contraint (see Eqs. (20-21)
in [SadErhStu12]_).
*variance* is used. In that case the fix parameter *deltamu* determines
the effective average constraint in the parallel VC-SGC MC algorithm
(parameter :math:`\delta\mu_0` in Eq. (20) of :ref:`Sadigh1
<Sadigh1>`). The parameter *kappa* specifies the variance constraint
(see Eqs. (20-21) in :ref:`Sadigh1 <Sadigh1>`).
The parameter *conc* sets the target concentration (parameter
:math:`c_0` in Eqs. (20-21) of [SadErhStu12]_). The atomic concentrations refer
to components `B`, `C` ..., with `A` being set automatically. When the
simulation includes `N` elements, `N-1` concentration values must be
specified.
:math:`c_0` in Eqs. (20-21) of :ref:`Sadigh1 <Sadigh1>`). The atomic
concentrations refer to components `B`, `C` ..., with `A` being set
automatically. When the simulation includes `N` elements, `N-1`
concentration values must be specified.
------------
@ -118,14 +118,15 @@ There are several technical parameters that can be set via optional flags.
*randseed* is expected to be a positive integer number and is used
to initialize the random number generator on each processor.
*window_size* controls the size of the sampling window in a parallel
MC simulation. The size has to lie between 0.5 and 1.0. Normally, this
parameter should be left unspecified which instructs the code to
choose the optimal window size automatically (see Sect. III.B and
Figure 6 in [SadErhStu12]_ for details).
*window_size* controls the size of the sampling window in a parallel MC
simulation. The size has to lie between 0.5 and 1.0. Normally, this
parameter should be left unspecified which instructs the code to choose
the optimal window size automatically (see Sect. III.B and Figure 6 in
:ref:`Sadigh1 <Sadigh1>` for details).
The number of times the window is moved during a MC cycle is set using the
parameter *window_moves* (see Sect. III.B in [SadErhStu12]_ for details).
The number of times the window is moved during a MC cycle is set using
the parameter *window_moves* (see Sect. III.B in :ref:`Sadigh1
<Sadigh1>` for details).
------------
@ -150,14 +151,18 @@ components of the vector represent the following quantities:
Restrictions
============
At present the fix provides optimized subroutines for EAM and CD-EAM type potentials
(see above) that calculate potential energy changes due to *local* atom type swaps
very efficiently.
Other potentials are supported by using the generic potential functions. This,
however, will lead to exceedingly slow simulations since the it implies that the
energy of the *entire* system is recomputed at each MC trial step.
If other potentials are to be used it is strongly recommended to modify and optimize
the existing generic potential functions for this purpose.
This fix is part of the MC package. It is only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
page for more info.
At present the fix provides optimized subroutines for EAM type
potentials (see above) that calculate potential energy changes due to
*local* atom type swaps very efficiently. Other potentials are
supported by using the generic potential functions. This, however, will
lead to exceedingly slow simulations since the it implies that the
energy of the *entire* system is recomputed at each MC trial step. If
other potentials are to be used it is strongly recommended to modify and
optimize the existing generic potential functions for this purpose.
------------
@ -169,3 +174,13 @@ The optional parameters default to the following values:
* *randseed* = 324234
* *window_moves* = 8
* *window_size* = automatic
------------
.. _Sadigh1:
**(Sadigh1)** B. Sadigh, P. Erhart, A. Stukowski, A. Caro, E. Martinez, and L. Zepeda-Ruiz, Phys. Rev. B **85**, 184203 (2012)
.. _Sadigh2:
**(Sadigh2)** B. Sadigh and P. Erhart, Phys. Rev. B **86**, 134204 (2012)

3
doc/utils/sphinx-config/false_positives.txt
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@ -692,6 +692,7 @@ delocalized
Delong
delr
deltaHf
deltamu
dem
Dendrimer
dendritic
@ -2500,6 +2501,7 @@ Nstart
nstats
Nstep
Nsteps
nsteps
nsteplast
Nstop
nsub
@ -3213,6 +3215,7 @@ setvel
sfftw
sfree
Sg
sgcmc
Shan
Shanno
Shapeev