diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 9017666417..bd3c2eca8e 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -360,7 +360,7 @@ accelerated styles exist. * :doc:`saed/vtk ` - time-average the intensities from :doc:`compute saed ` * :doc:`setforce ` - set the force on each atom * :doc:`setforce/spin ` - set magnetic precession vectors on each atom -* :doc:`sgcmc ` - fix for hybrid semi-grandcanonical MD/MC simulations +* :doc:`sgcmc ` - fix for hybrid semi-grand canonical MD/MC simulations * :doc:`shake ` - SHAKE constraints on bonds and/or angles * :doc:`shardlow ` - integration of DPD equations of motion using the Shardlow splitting * :doc:`smd ` - applied a steered MD force to a group diff --git a/doc/src/fix_sgcmc.rst b/doc/src/fix_sgcmc.rst index b51aed6b60..c9a5df2e98 100644 --- a/doc/src/fix_sgcmc.rst +++ b/doc/src/fix_sgcmc.rst @@ -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) `. Simulations can be carried out in either +the semi-grand canonical (SGC) or variance constrained semi-grand +canonical (VC-SGC) ensemble :ref:`(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 `) @@ -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 `). 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 +`). The parameter *kappa* specifies the variance constraint +(see Eqs. (20-21) in :ref:`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 `). 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 ` 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 +` 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 ` +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) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index ec7a54349d..faf8afdb31 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -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