updates "add eco df"
We think we followed all your requests/advice/suggestions (thanks!). We were unable to compile the current master (!) on Ubuntu and MacOS unless we added -std=c++11 to the Makefile(s) compiler flags. Note that this is NOT related to this pull request / the ECO Force. With this compiler flag, the current master works well with the fix_orient_eco (now renamed). The fix has been moved to USER-MISC (but we hope to get it to MISC later). We can't "make style_check ", but we have added our command to commands_fix.rst. We don't know GitHub well enough, so we don't know how to make sure that the PR #2122 was already included in the master, which we downloaded today.
This commit is contained in:
vmohles
@ -147,6 +147,7 @@ OPT.
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* :doc:`oneway <fix_oneway>`
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* :doc:`orient/bcc <fix_orient>`
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* :doc:`orient/fcc <fix_orient>`
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* :doc:`orient/eco <fix_orient_eco>`
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* :doc:`phonon <fix_phonon>`
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* :doc:`pimd <fix_pimd>`
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* :doc:`planeforce <fix_planeforce>`
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@ -1,26 +1,26 @@
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.. index:: fix eco/force
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.. index:: fix orient/eco
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fix eco/force command
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=====================
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fix orient/eco command
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======================
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.. parsed-literal::
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fix ID group-ID eco/force u0 eta rcut file
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fix ID group-ID orient/eco u0 eta rcut orientationsFile
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* ID, group-ID are documented in fix command
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* u0 = energy added to each atom (energy units)
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* eta = cutoff value (usually 0.25)
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* rcut = cutoff radius for orientation parameter calculation
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* file = file that specifies orientation of each grain
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* orientationsFile = file that specifies orientation of each grain
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix gb all eco/force 0.08 0.25 3.524 sigma5.ori
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fix gb all orient/eco 0.08 0.25 3.524 sigma5.ori
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Description
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@ -76,36 +76,37 @@ depends on the surrounding of this atom. An atom far from the grain boundary doe
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experience a synthetic force as its surrounding is that of an oriented single crystal
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and thermal fluctuations are masked by the parameter eta. Near the grain boundary
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however, the gradient is nonzero and synthetic force terms are computed.
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The orientation file specifies the perfect oriented crystal basis vectors for the
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two adjoining crystals. The first three lines for the energetically penalized and the
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The orientationsFile specifies the perfect oriented crystal basis vectors for the
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two adjoining crystals. The first three lines (line=row vector) for the energetically penalized and the
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last three lines for the energetically favored grain assuming u0 is positive. For
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negative u0 this is reversed. With the rcut parameter, the size of the region around
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each atom which is used in the order parameter computation is defined. It should at
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negative u0, this is reversed. With the rcut parameter, the size of the region around
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each atom which is used in the order parameter computation is defined. rcut must be
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smaller than the interaction range of the MD potential. It should at
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least include the nearest neighbor shell. For high temperatures or low angle
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grain boundaries, it might be beneficial to increase rcut in order to get a more
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precise identification of the atoms surrounding. However, computation time will
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increase as more atoms considered in the order parameter and force computation.
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increase as more atoms are considered in the order parameter and force computation.
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It is also worth noting that the cutoff radius must not exceed the communication
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distance for ghost atoms in LAMMPS. Currently however, the method stores results
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for order parameter and force computations in statically allocated arrays to
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increase efficiency such that the user is limited to 24 nearest neighbors.
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This is more than enough in most applications. With file, the input file for
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the 6 oriented crystal basis vectors is specified. Each line of the input file
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This is more than enough in most applications. With orientationsFile, the
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6 oriented crystal basis vectors is specified. Each line of the input file
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contains the three components of a primitive lattice vector oriented according to
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the grain orientation in the simulation box. The first (last) three lines correspond
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to the primitive lattice vectors of the first (second) grain. An example for
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a :math:`\Sigma\langle001\rangle` misorientation is given at the end.
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If no synthetic energy difference between the grains is created, u0=0, the
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force computation is omitted. In this case, the order parameter of the
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driving force can be used to track the grain boundary motion throughout the
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force computation is omitted. In this case, still, the order parameter of the
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driving force is computed and can be used to track the grain boundary motion throughout the
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simulation.
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**Restart, fix_modify, output, run start/stop, minimize info:**
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No information about this fix is written to :doc: `binary restart files`.
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No information about this fix is written to :doc: `binary restart files <restart>`.
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The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to
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add the potential energy of atom interactions with the grain boundary
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@ -113,7 +114,7 @@ driving force to the system's potential energy as part of thermodynamic output.
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The total sum of added synthetic potential energy is computed and can be accessed
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by various output options. The order parameter as well as the thermally masked
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output parameter are stored in per-atom arrays and can also be accessed by various
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output commands.
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:doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the start/stop keywords of the run command. This fix is
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not invoked during energy minimization.
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@ -123,7 +124,7 @@ not invoked during energy minimization.
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Restrictions
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""""""""""""
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This fix is part of the MISC package. It is only enabled if LAMMPS was
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This fix is part of the USER-MISC package. It is only enabled if LAMMPS was
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built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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@ -133,6 +134,8 @@ Related commands
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:doc:`fix_modify <fix_modify>`
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:doc:`fix_orient <fix_orient>`
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**Default:** none
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----------
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