mirror of https://github.com/lammps/lammps.git
Merge pull request #2230 from evoyiatzis/widom
Implementation of Widom insertions through a new fix widom command
This commit is contained in:
Axel Kohlmeyer
GitHub
commit
211beaee48
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@ -244,3 +244,4 @@ OPT.
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* :doc:`wall/region <fix_wall_region>`
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* :doc:`wall/region/ees <fix_wall_ees>`
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* :doc:`wall/srd <fix_wall_srd>`
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* :doc:`widom <fix_widom>`
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@ -387,6 +387,7 @@ accelerated styles exist.
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* :doc:`wall/region <fix_wall_region>` - use region surface as wall
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* :doc:`wall/region/ees <fix_wall_ees>` - use region surface as wall for ellipsoidal particles
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* :doc:`wall/srd <fix_wall_srd>` - slip/no-slip wall for SRD particles
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* :doc:`widom <fix_widom>` - Widom insertions of atoms or molecules
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Restrictions
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""""""""""""
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@ -68,7 +68,7 @@ Description
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This fix performs grand canonical Monte Carlo (GCMC) exchanges of
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atoms or molecules with an imaginary ideal gas
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reservoir at the specified T and chemical potential (mu) as discussed
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in :ref:`(Frenkel) <Frenkel>`. It also
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in :ref:`(Frenkel) <Frenkel2>`. It also
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attempts Monte Carlo (MC) moves (translations and molecule
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rotations) within the simulation cell or
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region. If used with the :doc:`fix nvt <fix_nh>`
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@ -481,7 +481,7 @@ listed above.
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----------
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.. _Frenkel:
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.. _Frenkel2:
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**(Frenkel)** Frenkel and Smit, Understanding Molecular Simulation,
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Academic Press, London, 2002.
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@ -0,0 +1,227 @@
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.. index:: fix widom
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fix widom 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 widom N M type seed T keyword values ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* widom = style name of this fix command
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* N = invoke this fix every N steps
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* M = number of Widom insertions to attempt every N steps
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* type = atom type for inserted atoms (must be 0 if mol keyword used)
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* seed = random # seed (positive integer)
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* T = temperature of the system (temperature units)
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* zero or more keyword/value pairs may be appended to args
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.. parsed-literal::
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keyword = *mol*\ , *region*\ , *full_energy*, *charge*\ , *intra_energy*
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*mol* value = template-ID
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template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
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*region* value = region-ID
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region-ID = ID of region where Widom insertions are allowed
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*full_energy* = compute the entire system energy when performing Widom insertions
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*charge* value = charge of inserted atoms (charge units)
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*intra_energy* value = intramolecular energy (energy units)
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 2 gas widom 1 50000 1 19494 2.0
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fix 3 water widom 1000 100 0 29494 300.0 mol h2omol full_energy
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Description
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"""""""""""
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This fix performs Widom insertions of atoms or molecules at the given
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temperature as discussed in :ref:`(Frenkel) <Frenkel1>`. Specific uses
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include computation of Henry constants of small molecules in microporous
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materials or amorphous systems.
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Every N timesteps the fix attempts M number of Widom insertions of atoms
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or molecules.
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If the *mol* keyword is used, only molecule insertions are performed.
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Conversely, if the *mol* keyword is not used, only atom insertions are
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performed.
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This command may optionally use the *region* keyword to define an
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insertion volume. The specified region must have been previously
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defined with a :doc:`region <region>` command. It must be defined with
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side = *in*\ . Insertion attempts occur only within the specified
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region. For non-rectangular regions, random trial points are generated
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within the rectangular bounding box until a point is found that lies
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inside the region. If no valid point is generated after 1000 trials, no
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insertion is performed. If an attempted insertion places the atom or
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molecule center-of-mass outside the specified region, a new attempted
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insertion is generated. This process is repeated until the atom or
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molecule center-of-mass is inside the specified region.
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Note that neighbor lists are re-built every timestep that this fix is
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invoked, so you should not set N to be too small. See the :doc:`neighbor
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<neighbor>` command for details.
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When an atom or molecule is to be inserted, its coordinates are chosen
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at a random position within the current simulation cell or region.
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Relative coordinates for atoms in a molecule are taken from the
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template molecule provided by the user. The center of mass of the
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molecule is placed at the insertion point. The orientation of the
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molecule is chosen at random by rotating about this point.
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Individual atoms are inserted, unless the *mol* keyword is used. It
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specifies a *template-ID* previously defined using the :doc:`molecule
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<molecule>` command, which reads a file that defines the molecule. The
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coordinates, atom types, charges, etc., as well as any bonding and
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special neighbor information for the molecule can be specified in the
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molecule file. See the :doc:`molecule <molecule>` command for details.
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The only settings required to be in this file are the coordinates and
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types of atoms in the molecule.
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If you wish to insert molecules via the *mol* keyword, that will have
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their bonds or angles constrained via SHAKE, use the *shake* keyword,
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specifying as its value the ID of a separate :doc:`fix shake
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<fix_shake>` command which also appears in your input script.
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Note that fix widom does not use configurational bias MC or any other
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kind of sampling of intramolecular degrees of freedom. Inserted
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molecules can have different orientations, but they will all have the
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same intramolecular configuration, which was specified in the molecule
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command input.
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For atoms, inserted particles have the specified atom type. For
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molecules, they use the same atom types as in the template molecule
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supplied by the user.
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The excess chemical potential mu_ex is defined as:
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.. math::
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\mu_{ex} = -kT \ln(<\exp(-(U_{N+1}-U_{N})/{kT})>)
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where *k* is Boltzman's constant, *T* is the user-specified temperature,
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U_N and U_{N+1} is the potential energy of the system with N and N+1
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particles.
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The *full_energy* option means that the fix calculates the total
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potential energy of the entire simulated system, instead of just the
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energy of the part that is changed. By default, this option is off, in
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which case only partial energies are computed to determine the energy
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difference due to the proposed change.
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The *full_energy* option is needed for systems with complicated
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potential energy calculations, including the following:
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* long-range electrostatics (kspace)
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* many-body pair styles
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* hybrid pair styles
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* eam pair styles
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* tail corrections
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* need to include potential energy contributions from other fixes
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In these cases, LAMMPS will automatically apply the *full_energy*
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keyword and issue a warning message.
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When the *mol* keyword is used, the *full_energy* option also includes
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the intramolecular energy of inserted and deleted molecules, whereas
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this energy is not included when *full_energy* is not used. If this is
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not desired, the *intra_energy* keyword can be used to define an amount
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of energy that is subtracted from the final energy when a molecule is
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inserted, and subtracted from the initial energy when a molecule is
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deleted. For molecules that have a non-zero intramolecular energy, this
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will ensure roughly the same behavior whether or not the *full_energy*
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option is used.
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Some fixes have an associated potential energy. Examples of such fixes
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include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
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:doc:`addforce <fix_addforce>`, :doc:`restrain <fix_restrain>`, and
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:doc:`wall fixes <fix_wall>`. For that energy to be included in the
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total potential energy of the system (the quantity used when performing
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Widom insertions), you MUST enable the :doc:`fix_modify <fix_modify>`
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*energy* option for that fix. The doc pages for individual :doc:`fix
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<fix>` commands specify if this should be done.
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Use the *charge* option to insert atoms with a user-specified point
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charge. Note that doing so will cause the system to become non-neutral.
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LAMMPS issues a warning when using long-range electrostatics (kspace)
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with non-neutral systems. See the :doc:`compute group/group
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<compute_group_group>` documentation for more details about simulating
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non-neutral systems with kspace on.
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**Restart, fix_modify, output, run start/stop, minimize info:**
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This fix writes the state of the fix to :doc:`binary restart files
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<restart>`. This includes information about the random number generator
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seed, the next timestep for Widom insertions etc. See the
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:doc:`read_restart <read_restart>` command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.
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.. note::
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For this to work correctly, the timestep must **not** be changed
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after reading the restart with :doc:`reset_timestep
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<reset_timestep>`. The fix will try to detect it and stop with an
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error.
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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 global vector of length 3, which can be accessed by
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various :doc:`output commands <Howto_output>`. The vector values are
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the following global cumulative quantities:
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* 1 = average excess chemical potential on each timestep
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* 2 = average difference in potential energy on each timestep
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* 3 = volume of the insertion region
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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
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:doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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This fix is part of the MC package. It is only enabled if LAMMPS was
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built with that package. See the :doc:`Build package <Build_package>`
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doc page for more info.
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Do not set "neigh_modify once yes" or else this fix will never be
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called. Reneighboring is **required**.
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Can be run in parallel, but aspects of the GCMC part will not scale well
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in parallel. Only usable for 3D simulations.
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Related commands
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""""""""""""""""
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:doc:`fix gcmc <fix_gcmc>`
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:doc:`fix atom/swap <fix_atom_swap>`,
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:doc:`neighbor <neighbor>`,
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:doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
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Default
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"""""""
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The option defaults are mol = no, intra_energy = 0.0 and full_energy =
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no, except for the situations where full_energy is required, as listed
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above.
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----------
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.. _Frenkel1:
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**(Frenkel)** Frenkel and Smit, Understanding Molecular Simulation,
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Academic Press, London, 2002.
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@ -3250,6 +3250,8 @@ whitesmoke
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whitespace
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Wi
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Wicaksono
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Widom
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widom
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Wijk
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Wikipedia
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wildcard
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@ -75,7 +75,7 @@ eim: NaCl using the EIM potential
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ellipse: ellipsoidal particles in spherical solvent, 2d system
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flow: Couette and Poiseuille flow in a 2d channel
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friction: frictional contact of spherical asperities between 2d surfaces
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gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
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gcmc: Grand Canonical MC with fix gcmc, Widom insertion with fix widom
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gjf: use of fix langevin Gronbech-Jensen/Farago option
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granregion: use of fix wall/region/gran as boundary on granular particles
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hugoniostat: Hugoniostat shock dynamics
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,28 @@
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# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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pair_modify shift yes
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read_data data.widom.lj
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 1 2 1.5 0.8 2.0
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pair_coeff 2 2 0.5 0.88 2.2
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neighbor 0.3 bin
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neigh_modify delay 0 every 5 check yes
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fix mywidom all widom 10 100000 2 29494 0.75
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fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
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fix 2 all nve
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timestep 0.002
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thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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thermo 10
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run 100
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@ -0,0 +1,38 @@
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units real
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dimension 3
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boundary p p p
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atom_style full
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pair_style lj/cut/coul/long 10.0
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bond_style harmonic
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angle_style harmonic
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read_data data.spce
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molecule h2omol H2O.txt
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### Flexible SPC/E Potential Parameters ###
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### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
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pair_coeff 1 1 0.1502629 3.1169
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pair_coeff 1 2 0.0341116368 2.04845
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pair_coeff 2 2 0.00774378 0.98
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bond_coeff 1 176.864 0.9611
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angle_coeff 1 42.1845 109.4712
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kspace_style pppm 1.0e-4
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fix mywidom all widom 10 20 0 29494 298 mol h2omol
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fix 2 all nvt temp 298.0 298.0 100.0
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neighbor 2.0 bin
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neigh_modify delay 10 every 2 check yes
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#run variables
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timestep 0.5
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thermo 10
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thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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run 100
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@ -0,0 +1,89 @@
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LAMMPS (30 Jun 2020)
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using 1 OpenMP thread(s) per MPI task
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# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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pair_modify shift yes
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read_data data.widom.lj
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orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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1000 atoms
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reading velocities ...
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1000 velocities
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read_data CPU = 0.003 seconds
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 1 2 1.5 0.8 2.0
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pair_coeff 2 2 0.5 0.88 2.2
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neighbor 0.3 bin
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neigh_modify delay 0 every 5 check yes
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fix mywidom all widom 10 100000 2 29494 0.75
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fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
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fix 2 all nve
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timestep 0.002
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thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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thermo 10
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run 100
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Neighbor list info ...
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update every 5 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
|
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bin: standard
|
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Per MPI rank memory allocation (min/avg/max) = 3.181 | 3.181 | 3.181 Mbytes
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Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
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10 0.7358936 -6.4405082 -5.3377717 7.1699962 830.584 1.2039721 -3.8577501 171.3429 830.584
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20 0.75426414 -6.4267946 -5.2965298 7.2833985 830.584 1.2039721 -4.0708206 227.63895 830.584
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30 0.72947489 -6.4064078 -5.3132896 7.3872583 830.584 1.2039721 -4.4304803 367.7146 830.584
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40 0.73504751 -6.4248725 -5.3234038 7.2927069 830.584 1.2039721 -4.1904189 266.99373 830.584
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50 0.76497439 -6.4352472 -5.2889331 7.3046861 830.584 1.2039721 -3.8628472 172.51133 830.584
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60 0.75752861 -6.4147051 -5.2795485 7.4416 830.584 1.2039721 -3.5355467 111.5042 830.584
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70 0.77775078 -6.4210798 -5.2556202 7.4473703 830.584 1.2039721 -3.4754802 102.92223 830.584
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80 0.80937104 -6.4320008 -5.2191583 7.4121087 830.584 1.2039721 -3.9287513 188.35625 830.584
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90 0.76321255 -6.4203633 -5.2766893 7.4307727 830.584 1.2039721 -4.2257529 279.87337 830.584
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100 0.74561743 -6.4010576 -5.2837499 7.52907 830.584 1.2039721 -3.6817835 135.5099 830.584
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Loop time of 25.8264 on 1 procs for 100 steps with 1000 atoms
|
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|
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Performance: 669.082 tau/day, 3.872 timesteps/s
|
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
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|
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MPI task timing breakdown:
|
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Section | min time | avg time | max time |%varavg| %total
|
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---------------------------------------------------------------
|
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Pair | 0.08186 | 0.08186 | 0.08186 | 0.0 | 0.32
|
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Neigh | 0.023613 | 0.023613 | 0.023613 | 0.0 | 0.09
|
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Comm | 0.0053532 | 0.0053532 | 0.0053532 | 0.0 | 0.02
|
||||
Output | 0.00037837 | 0.00037837 | 0.00037837 | 0.0 | 0.00
|
||||
Modify | 25.715 | 25.715 | 25.715 | 0.0 | 99.57
|
||||
Other | | 0.0005643 | | | 0.00
|
||||
|
||||
Nlocal: 1000.00 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3049.00 ave 3049 max 3049 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 46176.0 ave 46176 max 46176 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 46176
|
||||
Ave neighs/atom = 46.176000
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:25
|
||||
|
|
@ -0,0 +1,89 @@
|
|||
LAMMPS (30 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
read_data data.widom.lj
|
||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1000 atoms
|
||||
reading velocities ...
|
||||
1000 velocities
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.5 0.8 2.0
|
||||
pair_coeff 2 2 0.5 0.88 2.2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 5 check yes
|
||||
|
||||
fix mywidom all widom 10 100000 2 29494 0.75
|
||||
|
||||
fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
|
||||
fix 2 all nve
|
||||
|
||||
timestep 0.002
|
||||
|
||||
thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Neighbor list info ...
|
||||
update every 5 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.13 | 3.131 Mbytes
|
||||
Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
|
||||
10 0.74279259 -6.4332442 -5.3201696 7.2071344 830.584 1.2039721 -3.4462258 98.984938 830.584
|
||||
20 0.73016272 -6.4222911 -5.3281423 7.2714238 830.584 1.2039721 -4.4887329 397.41346 830.584
|
||||
30 0.74416342 -6.429139 -5.3140101 7.2713375 830.584 1.2039721 -4.3313574 322.19056 830.584
|
||||
40 0.73295457 -6.4370942 -5.3387618 7.227091 830.584 1.2039721 -4.7419281 557.00309 830.584
|
||||
50 0.76914235 -6.4473959 -5.2948361 7.2179148 830.584 1.2039721 -3.1794069 69.352982 830.584
|
||||
60 0.74099083 -6.4433012 -5.3329265 7.204973 830.584 1.2039721 -3.5231065 109.66994 830.584
|
||||
70 0.74514671 -6.4288463 -5.312244 7.2771269 830.584 1.2039721 -1.0154832 3.8727995 830.584
|
||||
80 0.72787097 -6.4457574 -5.3550427 7.1130709 830.584 1.2039721 -3.6691709 133.2501 830.584
|
||||
90 0.78452846 -6.5034376 -5.3278217 6.8238659 830.584 1.2039721 -2.0798339 16.008373 830.584
|
||||
100 0.77188499 -6.487313 -5.3306433 6.9133194 830.584 1.2039721 -2.066579 15.727938 830.584
|
||||
Loop time of 3.37748 on 4 procs for 100 steps with 1000 atoms
|
||||
|
||||
Performance: 5116.239 tau/day, 29.608 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.02025 | 0.020952 | 0.021322 | 0.3 | 0.62
|
||||
Neigh | 0.0059071 | 0.0060568 | 0.0061543 | 0.1 | 0.18
|
||||
Comm | 0.016558 | 0.059554 | 0.094282 | 12.2 | 1.76
|
||||
Output | 0.00022173 | 0.00042927 | 0.0010471 | 0.0 | 0.01
|
||||
Modify | 3.2552 | 3.2902 | 3.3335 | 1.7 | 97.42
|
||||
Other | | 0.0003003 | | | 0.01
|
||||
|
||||
Nlocal: 250.000 ave 256 max 242 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
Nghost: 1666.00 ave 1670 max 1659 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 11538.0 ave 11832 max 11091 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 46152
|
||||
Ave neighs/atom = 46.152000
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -0,0 +1,133 @@
|
|||
LAMMPS (30 Jun 2020)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
units real
|
||||
dimension 3
|
||||
boundary p p p
|
||||
atom_style full
|
||||
|
||||
pair_style lj/cut/coul/long 10.0
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
8640 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
5760 bonds
|
||||
reading angles ...
|
||||
2880 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.008 seconds
|
||||
read_data CPU = 0.028 seconds
|
||||
|
||||
molecule h2omol H2O.txt
|
||||
Read molecule template h2omol:
|
||||
1 molecules
|
||||
3 atoms with max type 2
|
||||
2 bonds with max type 1
|
||||
1 angles with max type 1
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
|
||||
### Flexible SPC/E Potential Parameters ###
|
||||
### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
|
||||
pair_coeff 1 1 0.1502629 3.1169
|
||||
pair_coeff 1 2 0.0341116368 2.04845
|
||||
pair_coeff 2 2 0.00774378 0.98
|
||||
|
||||
bond_coeff 1 176.864 0.9611
|
||||
angle_coeff 1 42.1845 109.4712
|
||||
kspace_style pppm 1.0e-4
|
||||
|
||||
fix mywidom all widom 10 20 0 29494 298 mol h2omol
|
||||
|
||||
fix 2 all nvt temp 298.0 298.0 100.0
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 10 every 2 check yes
|
||||
|
||||
|
||||
#run variables
|
||||
timestep 0.5
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:330)
|
||||
G vector (1/distance) = 0.2690183
|
||||
grid = 24 24 24
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.024843102
|
||||
estimated relative force accuracy = 7.4814263e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 29791 13824
|
||||
WARNING: Fix Widom using full_energy option (src/MC/fix_widom.cpp:297)
|
||||
0 atoms in group FixWidom:widom_exclusion_group:mywidom
|
||||
0 atoms in group FixWidom:rotation_gas_atoms:mywidom
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:487)
|
||||
Neighbor list info ...
|
||||
update every 2 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 8 8 8
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes
|
||||
Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
||||
0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.9140713 0 0 82468.116
|
||||
10 -29712.131 -31110.041 54.285179 -3154.4423 82468.116 1.9140713 241.93348 3.7366217e-178 82468.116
|
||||
20 -29711.939 -32614.429 112.71273 -4216.1592 82468.116 1.9140713 16.095006 1.5716469e-12 82468.116
|
||||
30 -29688.142 -32368.506 104.08688 -4093.6515 82468.116 1.9140713 5.7862327 5.7086352e-05 82468.116
|
||||
40 -29662.343 -32252.144 100.57005 -1458.5339 82468.116 1.9140713 126.68071 1.2467216e-93 82468.116
|
||||
50 -29646.78 -32837.635 123.91081 -4607.1155 82468.116 1.9140713 74.622397 1.8790479e-55 82468.116
|
||||
60 -29628.968 -33001.229 130.9554 -4589.5296 82468.116 1.9140713 3.6575433 0.0020780497 82468.116
|
||||
70 -29602.78 -32816.28 124.79023 -3082.1133 82468.116 1.9140713 13.983097 5.561247e-11 82468.116
|
||||
80 -29577.552 -33141.454 138.39742 -6332.8138 82468.116 1.9140713 41.98931 1.6075608e-31 82468.116
|
||||
90 -29550.865 -33792.115 164.70094 -4607.6419 82468.116 1.9140713 68.690681 4.2082269e-51 82468.116
|
||||
100 -29515.107 -34052.782 176.21207 -3609.5709 82468.116 1.9140713 41.090597 7.3326206e-31 82468.116
|
||||
Loop time of 163.407 on 1 procs for 100 steps with 8640 atoms
|
||||
|
||||
Performance: 0.026 ns/day, 907.819 hours/ns, 0.612 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.5495 | 8.5495 | 8.5495 | 0.0 | 5.23
|
||||
Bond | 0.031981 | 0.031981 | 0.031981 | 0.0 | 0.02
|
||||
Kspace | 2.3995 | 2.3995 | 2.3995 | 0.0 | 1.47
|
||||
Neigh | 5.0542 | 5.0542 | 5.0542 | 0.0 | 3.09
|
||||
Comm | 0.051965 | 0.051965 | 0.051965 | 0.0 | 0.03
|
||||
Output | 0.0018802 | 0.0018802 | 0.0018802 | 0.0 | 0.00
|
||||
Modify | 147.31 | 147.31 | 147.31 | 0.0 | 90.15
|
||||
Other | | 0.003614 | | | 0.00
|
||||
|
||||
Nlocal: 8640.00 ave 8640 max 8640 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 23499.0 ave 23499 max 23499 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3.27380e+06 ave 3.2738e+06 max 3.2738e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3273800
|
||||
Ave neighs/atom = 378.91204
|
||||
Ave special neighs/atom = 2.0000000
|
||||
Neighbor list builds = 220
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:44
|
||||
|
|
@ -493,11 +493,7 @@ void FixGCMC::init()
|
|||
}
|
||||
}
|
||||
|
||||
if (full_flag) {
|
||||
char *id_pe = (char *) "thermo_pe";
|
||||
int ipe = modify->find_compute(id_pe);
|
||||
c_pe = modify->compute[ipe];
|
||||
}
|
||||
if (full_flag) c_pe = modify->compute[modify->find_compute("thermo_pe")];
|
||||
|
||||
int *type = atom->type;
|
||||
|
||||
|
|
@ -580,18 +576,12 @@ void FixGCMC::init()
|
|||
// skip if already exists from previous init()
|
||||
|
||||
if (full_flag && !exclusion_group_bit) {
|
||||
char **group_arg = new char*[4];
|
||||
|
||||
// create unique group name for atoms to be excluded
|
||||
|
||||
int len = strlen(id) + 30;
|
||||
group_arg[0] = new char[len];
|
||||
sprintf(group_arg[0],"FixGCMC:gcmc_exclusion_group:%s",id);
|
||||
group_arg[1] = (char *) "subtract";
|
||||
group_arg[2] = (char *) "all";
|
||||
group_arg[3] = (char *) "all";
|
||||
group->assign(4,group_arg);
|
||||
exclusion_group = group->find(group_arg[0]);
|
||||
auto group_id = std::string("FixGCMC:gcmc_exclusion_group:") + id;
|
||||
group->assign(group_id + " subtract all all");
|
||||
exclusion_group = group->find(group_id);
|
||||
if (exclusion_group == -1)
|
||||
error->all(FLERR,"Could not find fix gcmc exclusion group ID");
|
||||
exclusion_group_bit = group->bitmask[exclusion_group];
|
||||
|
|
@ -603,34 +593,25 @@ void FixGCMC::init()
|
|||
char **arg = new char*[narg];;
|
||||
arg[0] = (char *) "exclude";
|
||||
arg[1] = (char *) "group";
|
||||
arg[2] = group_arg[0];
|
||||
arg[2] = (char *) group_id.c_str();
|
||||
arg[3] = (char *) "all";
|
||||
neighbor->modify_params(narg,arg);
|
||||
delete [] group_arg[0];
|
||||
delete [] group_arg;
|
||||
delete [] arg;
|
||||
}
|
||||
|
||||
// create a new group for temporary use with selected molecules
|
||||
|
||||
if (exchmode == EXCHMOL || movemode == MOVEMOL) {
|
||||
char **group_arg = new char*[3];
|
||||
|
||||
// create unique group name for atoms to be rotated
|
||||
int len = strlen(id) + 30;
|
||||
group_arg[0] = new char[len];
|
||||
sprintf(group_arg[0],"FixGCMC:rotation_gas_atoms:%s",id);
|
||||
group_arg[1] = (char *) "molecule";
|
||||
char digits[12];
|
||||
sprintf(digits,"%d",-1);
|
||||
group_arg[2] = digits;
|
||||
group->assign(3,group_arg);
|
||||
molecule_group = group->find(group_arg[0]);
|
||||
|
||||
auto group_id = std::string("FixGCMC:rotation_gas_atoms:") + id;
|
||||
group->assign(group_id + " molecule -1");
|
||||
molecule_group = group->find(group_id);
|
||||
if (molecule_group == -1)
|
||||
error->all(FLERR,"Could not find fix gcmc rotation group ID");
|
||||
molecule_group_bit = group->bitmask[molecule_group];
|
||||
molecule_group_inversebit = molecule_group_bit ^ ~0;
|
||||
delete [] group_arg[0];
|
||||
delete [] group_arg;
|
||||
}
|
||||
|
||||
// get all of the needed molecule data if exchanging
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,257 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(widom,FixWidom)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_WIDOM_H
|
||||
#define LMP_FIX_WIDOM_H
|
||||
|
||||
#include <cstdio>
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixWidom : public Fix {
|
||||
public:
|
||||
FixWidom(class LAMMPS *, int, char **);
|
||||
~FixWidom();
|
||||
int setmask();
|
||||
void init();
|
||||
void pre_exchange();
|
||||
|
||||
void attempt_atomic_insertion();
|
||||
void attempt_molecule_insertion();
|
||||
|
||||
void attempt_atomic_insertion_full();
|
||||
void attempt_molecule_insertion_full();
|
||||
double energy(int, int, tagint, double *);
|
||||
double molecule_energy(tagint);
|
||||
double energy_full();
|
||||
void update_gas_atoms_list();
|
||||
double compute_vector(int);
|
||||
double memory_usage();
|
||||
void write_restart(FILE *);
|
||||
void restart(char *);
|
||||
void grow_molecule_arrays(int);
|
||||
|
||||
private:
|
||||
int molecule_group,molecule_group_bit;
|
||||
int molecule_group_inversebit;
|
||||
int exclusion_group,exclusion_group_bit;
|
||||
int nwidom_type,nevery,seed;
|
||||
int ninsertions;
|
||||
int ngas; // # of gas atoms on all procs
|
||||
int ngas_local; // # of gas atoms on this proc
|
||||
int exchmode; // exchange ATOM or MOLECULE
|
||||
int movemode; // move ATOM or MOLECULE
|
||||
int regionflag; // 0 = anywhere in box, 1 = specific region
|
||||
int iregion; // widom region
|
||||
char *idregion; // widom region id
|
||||
bool charge_flag; // true if user specified atomic charge
|
||||
bool full_flag; // true if doing full system energy calculations
|
||||
|
||||
int natoms_per_molecule; // number of atoms in each inserted molecule
|
||||
int nmaxmolatoms; // number of atoms allocated for molecule arrays
|
||||
|
||||
double ave_widom_chemical_potential;
|
||||
|
||||
int widom_nmax;
|
||||
int max_region_attempts;
|
||||
double gas_mass;
|
||||
double insertion_temperature;
|
||||
double beta,sigma,volume;
|
||||
double charge;
|
||||
double xlo,xhi,ylo,yhi,zlo,zhi;
|
||||
double region_xlo,region_xhi,region_ylo,region_yhi,region_zlo,region_zhi;
|
||||
double region_volume;
|
||||
double energy_stored; // full energy of old/current configuration
|
||||
double *sublo,*subhi;
|
||||
int *local_gas_list;
|
||||
double **cutsq;
|
||||
double **molcoords;
|
||||
double *molq;
|
||||
imageint *molimage;
|
||||
imageint imagezero;
|
||||
|
||||
double energy_intra;
|
||||
|
||||
class Pair *pair;
|
||||
|
||||
class RanPark *random_equal;
|
||||
|
||||
class Atom *model_atom;
|
||||
|
||||
class Molecule **onemols;
|
||||
int imol,nmol;
|
||||
int triclinic; // 0 = orthog box, 1 = triclinic
|
||||
|
||||
class Compute *c_pe;
|
||||
|
||||
void options(int, char **);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Fix Widom does not (yet) work with atom_style template
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix Widom region does not support a bounding box
|
||||
|
||||
Not all regions represent bounded volumes. You cannot use
|
||||
such a region with the fix Widom command.
|
||||
|
||||
E: Fix Widom region cannot be dynamic
|
||||
|
||||
Only static regions can be used with fix Widom.
|
||||
|
||||
E: Fix Widom region extends outside simulation box
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix Widom molecule must have coordinates
|
||||
|
||||
The defined molecule does not specify coordinates.
|
||||
|
||||
E: Fix Widom molecule must have atom types
|
||||
|
||||
The defined molecule does not specify atom types.
|
||||
|
||||
E: Atom type must be zero in fix Widom mol command
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix Widom molecule has charges, but atom style does not
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix Widom molecule template ID must be same as atom_style template ID
|
||||
|
||||
When using atom_style template, you cannot insert molecules that are
|
||||
not in that template.
|
||||
|
||||
E: Fix Widom atom has charge, but atom style does not
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Molecule template ID for fix Widom does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
W: Molecule template for fix Widom has multiple molecules
|
||||
|
||||
The fix Widom command will only create molecules of a single type,
|
||||
i.e. the first molecule in the template.
|
||||
|
||||
E: Region ID for fix Widom does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
W: Fix Widom using full_energy option
|
||||
|
||||
Fix Widom has automatically turned on the full_energy option since it
|
||||
is required for systems like the one specified by the user. User input
|
||||
included one or more of the following: kspace, a hybrid
|
||||
pair style, an eam pair style, tail correction,
|
||||
or no "single" function for the pair style.
|
||||
|
||||
E: Invalid atom type in fix Widom command
|
||||
|
||||
The atom type specified in the Widom command does not exist.
|
||||
|
||||
E: Fix Widom cannot exchange individual atoms belonging to a molecule
|
||||
|
||||
This is an error since you should not delete only one atom of a
|
||||
molecule. The user has specified atomic (non-molecular) gas
|
||||
exchanges, but an atom belonging to a molecule could be deleted.
|
||||
|
||||
E: All mol IDs should be set for fix Widom group atoms
|
||||
|
||||
The molecule flag is on, yet not all molecule ids in the fix group
|
||||
have been set to non-zero positive values by the user. This is an
|
||||
error since all atoms in the fix Widom group are eligible for deletion,
|
||||
rotation, and translation and therefore must have valid molecule ids.
|
||||
|
||||
E: Fix Widom molecule command requires that atoms have molecule attributes
|
||||
|
||||
Should not choose the Widom molecule feature if no molecules are being
|
||||
simulated. The general molecule flag is off, but Widom's molecule flag
|
||||
is on.
|
||||
|
||||
E: Cannot use fix Widom in a 2d simulation
|
||||
|
||||
Fix Widom is set up to run in 3d only. No 2d simulations with fix Widom
|
||||
are allowed.
|
||||
|
||||
E: Could not find fix Widom exclusion group ID
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Illegal fix Widom gas mass <= 0
|
||||
|
||||
The computed mass of the designated gas molecule or atom type was less
|
||||
than or equal to zero.
|
||||
|
||||
E: Cannot do Widom on atoms in atom_modify first group
|
||||
|
||||
This is a restriction due to the way atoms are organized in a list to
|
||||
enable the atom_modify first command.
|
||||
|
||||
W: Fix Widom is being applied to the default group all
|
||||
|
||||
This is allowed, but it will result in Monte Carlo moves
|
||||
being performed on all the atoms in the system, which is
|
||||
often not what is intended.
|
||||
|
||||
E: Could not find specified fix Widom group ID
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: fix Widom does currently not support full_energy option with molecules on more than 1 MPI process.
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Fix Widom put atom outside box
|
||||
|
||||
This should not normally happen. Contact the developers.
|
||||
|
||||
E: Fix Widom ran out of available molecule IDs
|
||||
|
||||
See the setting for tagint in the src/lmptype.h file.
|
||||
|
||||
E: Fix Widom ran out of available atom IDs
|
||||
|
||||
See the setting for tagint in the src/lmptype.h file.
|
||||
|
||||
E: Too many total atoms
|
||||
|
||||
See the setting for bigint in the src/lmptype.h file.
|
||||
|
||||
*/
|
||||
|
|
@ -584,10 +584,10 @@ void Group::create(char *name, int *flag)
|
|||
return group index if name matches existing group, -1 if no such group
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int Group::find(const char *name)
|
||||
int Group::find(const std::string &name)
|
||||
{
|
||||
for (int igroup = 0; igroup < MAX_GROUP; igroup++)
|
||||
if (names[igroup] && strcmp(name,names[igroup]) == 0) return igroup;
|
||||
if (names[igroup] && (name == names[igroup])) return igroup;
|
||||
return -1;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -33,7 +33,7 @@ class Group : protected Pointers {
|
|||
void assign(int, char **); // assign atoms to a group
|
||||
void assign(const std::string &); // convenience function
|
||||
void create(char *, int *); // add flagged atoms to a group
|
||||
int find(const char *); // lookup name in list of groups
|
||||
int find(const std::string &); // lookup name in list of groups
|
||||
int find_or_create(const char *); // lookup name or create new group
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
|
|
|
|||
Loading…
Reference in New Issue