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documentation intergration and fixes

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This commit is contained in:
Axel Kohlmeyer
2023-12-15 18:48:27 -05:00
parent 51b38c5b24
commit 5506f42005
3 changed files with 11 additions and 16 deletions
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1
doc/src/Commands_fix.rst
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@ -95,6 +95,7 @@ OPT.
* :doc:`halt <fix_halt>`
* :doc:`heat <fix_heat>`
* :doc:`heat/flow <fix_heat_flow>`
* :doc:`hmc <fix_hmc>`
* :doc:`hyper/global <fix_hyper_global>`
* :doc:`hyper/local <fix_hyper_local>`
* :doc:`imd <fix_imd>`

1
doc/src/fix.rst
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@ -260,6 +260,7 @@ accelerated styles exist.
* :doc:`halt <fix_halt>` - terminate a dynamics run or minimization
* :doc:`heat <fix_heat>` - add/subtract momentum-conserving heat
* :doc:`heat/flow <fix_heat_flow>` - plain time integration of heat flow with per-atom temperature updates
* :doc:`hmc <fix_hmc>` - Hybrid/Hamiltonian Monte Carlo (HMC) particle propagation
* :doc:`hyper/global <fix_hyper_global>` - global hyperdynamics
* :doc:`hyper/local <fix_hyper_local>` - local hyperdynamics
* :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol

25
doc/src/fix_hmc.rst
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@ -1,7 +1,7 @@
fix hmc command
==============================
.. index:: fix hmc
Accelerator Variants: *None*
fix hmc command
===============
Syntax
""""""
@ -21,7 +21,7 @@ Syntax
*mom* value = *yes* or *no*
*ra* value = *yes* or *no*
Examples
""""""""
@ -33,21 +33,21 @@ Examples
Description
"""""""""""
This fix performs the the Hybrid/Hamiltonian Monte Carlo (HMC)algorithm
.. versionadded:: TBD
This fix performs the the Hybrid/Hamiltonian Monte Carlo (HMC) algorithm
in line with the following order of steps:
The new particle configuration (positions and velocities) is calculated
by invoking the velocity-Verlet time integration algorithm.
Before these configuration changes are performed, the proposed change
in the Hamiltonian,
:math:`\Delta{H}`
is calculated following the equation:
in the Hamiltonian, :math:`\Delta{H}` is calculated following the equation:
.. math::
\Delta{H} = H(q′,p′) - H(q,p)
This new proposed configuration is then accepted/rejected according to
the Metropolis criterion with probability:
@ -109,10 +109,3 @@ The option default is mom = yes, ra = no.
**(Metropolis)** Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. The journal of chemical physics
1953, 21, 1087–1092.
LAMMPS Developers Issue 565: [Brief description of the issue] GitHub issue, https://github.com/lammps/
lammps/issues/565.
LAMMPS Development Team LAMMPS Documentation: Modify Requirements https://docs.lammps.org/
Modify_requirements.html.