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.. index:: compute angle
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compute angle command
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=====================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID angle
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* angle = style name of this compute command
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Examples
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""""""""
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.. parsed-literal::
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compute 1 all angle
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Description
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"""""""""""
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Define a computation that extracts the angle energy calculated by each
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of the angle sub-styles used in the "angle_style
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hybrid" angle_hybrid.html command. These values are made accessible
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for output or further processing by other commands. The group
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specified for this command is ignored.
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This compute is useful when using :doc:`angle_style hybrid <angle_hybrid>` if you want to know the portion of the total
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energy contributed by one or more of the hybrid sub-styles.
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**Output info:**
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This compute calculates a global vector of length N where N is the
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number of sub_styles defined by the :doc:`angle_style hybrid <angle_style>` command, which can be accessed by indices
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1-N. These values can be used by any command that uses global scalar
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or vector values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output
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options.
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The vector values are "extensive" and will be in energy
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:doc:`units <units>`.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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@ -1,59 +0,0 @@
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.. index:: compute dihedral
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compute dihedral command
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========================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID dihedral
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* dihedral = style name of this compute command
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Examples
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""""""""
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.. parsed-literal::
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compute 1 all dihedral
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Description
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"""""""""""
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Define a computation that extracts the dihedral energy calculated by
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each of the dihedral sub-styles used in the :doc:`dihedral_style hybrid <dihedral_hybrid>` command. These values are made
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accessible for output or further processing by other commands. The
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group specified for this command is ignored.
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This compute is useful when using :doc:`dihedral_style hybrid <dihedral_hybrid>` if you want to know the portion of the
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total energy contributed by one or more of the hybrid sub-styles.
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**Output info:**
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This compute calculates a global vector of length N where N is the
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number of sub_styles defined by the :doc:`dihedral_style hybrid <dihedral_style>` command. which can be accessed by indices
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1-N. These values can be used by any command that uses global scalar
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or vector values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output
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options.
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The vector values are "extensive" and will be in energy
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:doc:`units <units>`.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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@ -1,59 +0,0 @@
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.. index:: compute improper
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compute improper command
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========================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID improper
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* improper = style name of this compute command
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Examples
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""""""""
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.. parsed-literal::
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compute 1 all improper
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Description
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"""""""""""
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Define a computation that extracts the improper energy calculated by
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each of the improper sub-styles used in the :doc:`improper_style hybrid <improper_hybrid>` command. These values are made
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accessible for output or further processing by other commands. The
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group specified for this command is ignored.
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This compute is useful when using :doc:`improper_style hybrid <improper_hybrid>` if you want to know the portion of the
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total energy contributed by one or more of the hybrid sub-styles.
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**Output info:**
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This compute calculates a global vector of length N where N is the
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number of sub_styles defined by the :doc:`improper_style hybrid <improper_style>` command. which can be accessed by indices
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1-N. These values can be used by any command that uses global scalar
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or vector values from a compute as input. See :ref:`this section <howto_15>` for an overview of LAMMPS output
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options.
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The vector values are "extensive" and will be in energy
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:doc:`units <units>`.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`compute pe <compute_pe>`, :doc:`compute pair <compute_pair>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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.. index:: fix shardlow
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fix shardlow command
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====================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID shardlow
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* shardlow = style name of this fix command
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Examples
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""""""""
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.. parsed-literal::
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fix 1 all shardlow
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Description
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"""""""""""
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Specifies that the Shardlow splitting algorithm (SSA) is to be used to
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integrate the DPD equations of motion. The SSA splits the integration
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into a stochastic and deterministic integration step. The fix
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*shardlow* performs the stochastic integration step and must be used
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in conjunction with a deterministic integrator (e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nph>`). The stochastic
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integration of the dissipative and random forces is performed prior to
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the deterministic integration of the conservative force. Further
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details regarding the method are provided in :ref:`(Lisal) <Lisal>` and
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:ref:`(Larentzos) <Larentzos>`.
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The fix *shardlow* must be used with the :doc:`pair_style dpd/fdt <pair_style>` or :doc:`pair_style dpd/fdt/energy <pair_style>` command to properly initialize the
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fluctuation-dissipation theorem parameter(s) sigma (and kappa, if
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necessary).
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Note that numerous variants of DPD can be specified by choosing an
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appropriate combination of the integrator and :doc:`pair_style dpd/fdt <pair_style>` command. DPD under isothermal conditions can
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be specified by using fix *shardlow*, fix *nve* and pair_style
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*dpd/fdt*. DPD under isoenergetic conditions can be specified by
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using fix *shardlow*, fix *nve* and pair_style *dpd/fdt/energy*. DPD
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under isobaric conditions can be specified by using fix shardlow, fix
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*nph* and pair_style *dpd/fdt*. DPD under isoenthalpic conditions can
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be specified by using fix shardlow, fix *nph* and pair_style
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*dpd/fdt/energy*. Examples of each DPD variant are provided in the
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examples/USER/dpd directory.
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----------
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Restrictions
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""""""""""""
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This fix is only available if LAMMPS is built with the USER-DPD
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package. See the :ref:`Making LAMMPS <start_3>` section
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for more info.
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This fix is currently limited to orthogonal simulation cell
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geometries.
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This fix must be used with an additional fix that specifies time
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integration, e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`.
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The Shardlow splitting algorithm requires the sizes of the sub-domain
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lengths to be larger than twice the cutoff+skin. Generally, the
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domain decomposition is dependant on the number of processors
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requested.
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Related commands
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""""""""""""""""
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:doc:`pair_style dpd/fdt <pair_dpd_fdt>`, :doc:`fix eos/cv <fix_eos_cv>`
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**Default:** none
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----------
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.. _Lisal:
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**(Lisal)** M. Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative
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particle dynamics as isothermal, isobaric, isoenergetic, and
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isoenthalpic conditions using Shardlow-like splitting algorithms.",
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J. Chem. Phys., 135, 204105 (2011).
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.. _Larentzos:
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**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and
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W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic
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Dissipative Particle Dynamics Using Shardlow-Like Splitting
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Algorithms", Comput. Phys. Commun., 185, 1987-1998 (2014).
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.. _Larentzos:
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**(Larentzos)** J.P. Larentzos, J.K. Brennan, J.D. Moore, and
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W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative
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Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
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Laboratory, Aberdeen Proving Ground, MD (2014).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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168
doc/fix_smd.rst
168
doc/fix_smd.rst
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.. index:: fix smd
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fix smd command
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===============
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID smd type values keyword values
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* smd = style name of this fix command
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* mode = *cvel* or *cfor* to select constant velocity or constant force SMD
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.. parsed-literal::
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*cvel* values = K vel
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K = spring constant (force/distance units)
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vel = velocity of pulling (distance/time units)
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*cfor* values = force
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force = pulling force (force units)
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* keyword = *tether* or *couple*
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.. parsed-literal::
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*tether* values = x y z R0
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x,y,z = point to which spring is tethered
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R0 = distance of end of spring from tether point (distance units)
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*couple* values = group-ID2 x y z R0
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group-ID2 = 2nd group to couple to fix group with a spring
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x,y,z = direction of spring, automatically computed with 'auto'
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R0 = distance of end of spring (distance units)
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Examples
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""""""""
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.. parsed-literal::
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fix pull cterm smd cvel 20.0 -0.00005 tether NULL NULL 100.0 0.0
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fix pull cterm smd cvel 20.0 -0.0001 tether 25.0 25 25.0 0.0
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fix stretch cterm smd cvel 20.0 0.0001 couple nterm auto auto auto 0.0
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fix pull cterm smd cfor 5.0 tether 25.0 25.0 25.0 0.0
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Description
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"""""""""""
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This fix implements several options of steered MD (SMD) as reviewed in
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:ref:`(Izrailev) <Izrailev>`, which allows to induce conformational changes
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in systems and to compute the potential of mean force (PMF) along the
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assumed reaction coordinate :ref:`(Park) <Park>` based on Jarzynski's
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equality :ref:`(Jarzynski) <Jarzynski>`. This fix borrows a lot from :doc:`fix spring <fix_spring>` and :doc:`fix setforce <fix_setforce>`.
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You can apply a moving spring force to a group of atoms (*tether*
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style) or between two groups of atoms (*couple* style). The spring
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can then be used in either constant velocity (*cvel*) mode or in
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constant force (*cfor*) mode to induce transitions in your systems.
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When running in *tether* style, you may need some way to fix some
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other part of the system (e.g. via :doc:`fix spring/self <fix_spring_self>`)
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The *tether* style attaches a spring between a point at a distance of
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R0 away from a fixed point *x,y,z* and the center of mass of the fix
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group of atoms. A restoring force of magnitude K (R - R0) Mi / M is
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applied to each atom in the group where *K* is the spring constant, Mi
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is the mass of the atom, and M is the total mass of all atoms in the
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group. Note that *K* thus represents the total force on the group of
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atoms, not a per-atom force.
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In *cvel* mode the distance R is incremented or decremented
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monotonously according to the pulling (or pushing) velocity.
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In *cfor* mode a constant force is added and the actual distance
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in direction of the spring is recorded.
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The *couple* style links two groups of atoms together. The first
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group is the fix group; the second is specified by group-ID2. The
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groups are coupled together by a spring that is at equilibrium when
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the two groups are displaced by a vector in direction *x,y,z* with
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respect to each other and at a distance R0 from that displacement.
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Note that *x,y,z* only provides a direction and will be internally
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normalized. But since it represents the *absolute* displacement of
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group-ID2 relative to the fix group, (1,1,0) is a different spring
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than (-1,-1,0). For each vector component, the displacement can be
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described with the *auto* parameter. In this case the direction is
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recomputed in every step, which can be useful for steering a local
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process where the whole object undergoes some other change. When the
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relative positions and distance between the two groups are not in
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equilibrium, the same spring force described above is applied to atoms
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in each of the two groups.
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For both the *tether* and *couple* styles, any of the x,y,z values can
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be specified as NULL which means do not include that dimension in the
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distance calculation or force application.
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For constant velocity pulling (*cvel* mode), the running integral
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over the pulling force in direction of the spring is recorded and
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can then later be used to compute the potential of mean force (PMF)
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by averaging over multiple independent trajectories along the same
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pulling path.
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Restart, fix_modify, output, run start/stop, minimize info
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""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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The fix stores the direction of the spring, current pulling target
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distance and the running PMF to :doc:`binary restart files <restart>`.
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See the :doc:`read_restart <read_restart>` command for info on how to
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re-specify a fix in an input script that reads a restart file, so that
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the operation of the fix continues in an uninterrupted fashion.
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None of the :doc:`fix_modify <fix_modify>` options are relevant to this
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fix.
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This fix computes a vector list of 7 quantities, which can be accessed
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by various :ref:`output commands <howto_15>`. The
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quantities in the vector are in this order: the x-, y-, and
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z-component of the pulling force, the total force in direction of the
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pull, the equilibrium distance of the spring, the distance between the
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two reference points, and finally the accumulated PMF (the sum of
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pulling forces times displacement).
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The force is the total force on the group of atoms by the spring. In
|
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the case of the *couple* style, it is the force on the fix group
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(group-ID) or the negative of the force on the 2nd group (group-ID2).
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The vector values calculated by this fix are "extensive".
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
|
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|
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|
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This fix is part of the USER-MISC package. It is only enabled if
|
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LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
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Related commands
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""""""""""""""""
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:doc:`fix drag <fix_drag>`, :doc:`fix spring <fix_spring>`,
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:doc:`fix spring/self <fix_spring_self>`,
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:doc:`fix spring/rg <fix_spring_rg>`
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|
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**Default:** none
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----------
|
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|
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.. _Israilev:
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**(Izrailev)** Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar,
|
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Wriggers, Schulten. Computational Molecular Dynamics: Challenges,
|
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Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
|
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Engineering, pp. 39-65. Springer-Verlag, Berlin, 1998.
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**(Park)**
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Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
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**(Jarzynski)**
|
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Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
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|
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
|
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.. _lc: Section_commands.html#comm
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Reference in New Issue