reorder punctuation and quotation characters for clarity
This commit is contained in:
Axel Kohlmeyer
@ -1373,7 +1373,7 @@ Bibliography
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Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
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**(Ziegler)**
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J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
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J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
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**(Zimmerman2004)**
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Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.
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@ -276,7 +276,7 @@ the barostat as outlined in:
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N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
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accurately describe the structure, pressure, and compressibility of
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molecular liquids," J. Chem. Phys. 143, 243148 (2015).
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molecular liquids", J. Chem. Phys. 143, 243148 (2015).
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**Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The
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Pennsylvania State University)
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@ -495,7 +495,7 @@ run:
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write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
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Note that the specified restartfile and dumpfile names may contain
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wild-card characters ("\*","%") as explained on the
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wild-card characters ("\*" or "%") as explained on the
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:doc:`read_restart <read_restart>` and :doc:`write_dump <write_dump>` doc
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pages. The use of "%" means that a parallel restart file and/or
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parallel dump file can be read and/or written. Note that a filename
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@ -536,6 +536,6 @@ supported.
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References
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""""""""""
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* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
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* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
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* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
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* Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.
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@ -78,7 +78,7 @@ These values can be accessed by any command that uses global array
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values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
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options.
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The array values are "intensive." The array values will be in
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The array values are "intensive". The array values will be in
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mass-velocity-distance :doc:`units <units>`.
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Restrictions
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@ -182,7 +182,7 @@ by any command that uses global values from a compute as input. See
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the :doc:`Howto output <Howto_output>` doc page for an overview of
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LAMMPS output options.
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The array values calculated by this compute are all "extensive."
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The array values calculated by this compute are all "extensive".
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Restrictions
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""""""""""""
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@ -49,7 +49,7 @@ accessed by indices 1--3 by any command that uses global vector values
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from a compute as input. See the :doc:`Howto output <Howto_output>` doc
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page for an overview of LAMMPS output options.
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|
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The vector values are "intensive." The vector values will be in
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The vector values are "intensive". The vector values will be in
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distance :doc:`units <units>`.
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Restrictions
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@ -77,7 +77,7 @@ values can be accessed by any command that uses global array values
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from a compute as input. See the :doc:`Howto output <Howto_output>` doc
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page for an overview of LAMMPS output options.
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|
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The array values are "intensive." The array values will be in
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The array values are "intensive". The array values will be in
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distance :doc:`units <units>`.
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Restrictions
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@ -54,7 +54,7 @@ the computed dipole moment and a global vector of length 3 with the
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dipole vector. See the :doc:`Howto output <Howto_output>` page for
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an overview of LAMMPS output options.
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The computed values are "intensive." The array values will be in
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The computed values are "intensive". The array values will be in
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dipole units (i.e., charge :doc:`units <units>` times distance
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:doc:`units <units>`).
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@ -86,7 +86,7 @@ chunk. These values can be accessed by any command that uses global
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array values from a compute as input. See the :doc:`Howto output
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<Howto_output>` page for an overview of LAMMPS output options.
|
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The array values are "intensive." The array values will be in
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The array values are "intensive". The array values will be in
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dipole units (i.e., charge :doc:`units <units>` times distance
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:doc:`units <units>`).
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@ -48,7 +48,7 @@ used by any command that uses a global scalar value from a compute as
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input. See the :doc:`Howto output <Howto_output>` page for an
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overview of LAMMPS output options.
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The scalar value calculated by this compute is "extensive." The
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The scalar value calculated by this compute is "extensive". The
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scalar value will be in energy :doc:`units <units>`.
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Restrictions
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@ -48,7 +48,7 @@ of all the rigid bodies). This value can be used by any command that
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uses a global scalar value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
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options.
|
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|
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The scalar value calculated by this compute is "extensive." The
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The scalar value calculated by this compute is "extensive". The
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scalar value will be in energy :doc:`units <units>`.
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Restrictions
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@ -44,7 +44,7 @@ used by any command that uses a global scalar value from a compute as
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input. See the :doc:`Howto output <Howto_output>` page for an
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overview of LAMMPS output options.
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|
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The scalar value calculated by this compute is "extensive." The
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The scalar value calculated by this compute is "extensive". The
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scalar value will be in energy :doc:`units <units>`.
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Restrictions
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@ -40,7 +40,7 @@ further than the threshold distance.
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If the system is undergoing significant center-of-mass motion,
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due to thermal motion, an external force, or an initial net momentum,
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then this compute will not be able to distinguish that motion from
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local atom displacements and may generate "false positives."
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local atom displacements and may generate "false positives".
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Output info
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"""""""""""
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@ -50,7 +50,7 @@ used by any command that uses a global scalar value from a compute as
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input. See the :doc:`Howto output <Howto_output>` page for an
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overview of LAMMPS output options.
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||||
|
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The scalar value calculated by this compute is "intensive." The
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The scalar value calculated by this compute is "intensive". The
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scalar value will be a 0 or 1 as explained above.
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Restrictions
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@ -299,7 +299,7 @@ These output results can be used by any command that uses a global
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scalar or vector from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
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options. For example, the computed values can be averaged using :doc:`fix ave/time <fix_ave_time>`.
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||||
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The values calculated by this compute are "extensive."
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The values calculated by this compute are "extensive".
|
||||
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Restrictions
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""""""""""""
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||||
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@ -140,7 +140,7 @@ vector values from a compute as input. See the
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options.
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Both the scalar and vector values calculated by this compute are
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"extensive." The scalar value will be in energy :doc:`units <units>`.
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"extensive". The scalar value will be in energy :doc:`units <units>`.
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The vector values will be in force :doc:`units <units>`.
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Restrictions
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||||
|
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@ -69,7 +69,7 @@ vector values from a compute as input. See the :doc:`Howto output <Howto_output
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options.
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The scalar and vector values calculated by this compute are
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"intensive." The scalar and vector values will be in distance and
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"intensive". The scalar and vector values will be in distance and
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distance\ :math:`^2` :doc:`units <units>`, respectively.
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Restrictions
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||||
|
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@ -78,7 +78,7 @@ vector values from a compute as input. See the
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options.
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The vector values calculated by this compute are
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"intensive." The first five vector values will be in
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"intensive". The first five vector values will be in
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distance\ :math:`2` :doc:`units <units>` while the sixth one is dimensionless.
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|
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Restrictions
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||||
|
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@ -80,7 +80,7 @@ See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
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output options.
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The array calculated by this compute is
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"intensive." The first five columns will be in
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"intensive". The first five columns will be in
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distance\ :math:`^2` :doc:`units <units>` while the sixth one is dimensionless.
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|
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Restrictions
|
||||
|
||||
@ -142,14 +142,14 @@ command that uses global vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` documentation for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The vector values calculated by this compute are "extensive," meaning
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The vector values calculated by this compute are "extensive", meaning
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they scale with the number of atoms in the simulation. They can be
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divided by the appropriate volume to get a flux, which would then be
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an "intensive" value, meaning independent of the number of atoms in
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the simulation. Note that if the compute is "all," then the
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appropriate volume to divide by is the simulation box volume.
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However, if a sub-group is used, it should be the volume containing
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those atoms.
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divided by the appropriate volume to get a flux, which would then be an
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||||
"intensive" value, meaning independent of the number of atoms in the
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simulation. Note that if the compute group is "all", then the
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appropriate volume to divide by is the simulation box volume. However,
|
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if a group with a subset of atoms is used, it should be the volume
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containing those atoms.
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||||
|
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The vector values will be in energy\*velocity :doc:`units <units>`. Once
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||||
divided by a volume the units will be that of flux, namely
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@ -172,7 +172,7 @@ requested as arguments to the command (the potential energy, pressure and/or hea
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capacity). The elements of the vector can be accessed by indices 1--n by any
|
||||
command that uses global vector values as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values calculated by this compute are "extensive." The
|
||||
The vector values calculated by this compute are "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -84,7 +84,7 @@ by any command that uses global array values from a compute as input. See the
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||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
mass\*distance\ :math:`^2` :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -52,7 +52,7 @@ can be used by any command that uses a global scalar value from a
|
||||
compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive." The
|
||||
The scalar value calculated by this compute is "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -48,7 +48,7 @@ global scalar value from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive." The
|
||||
The scalar value calculated by this compute is "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -37,7 +37,7 @@ length 3. This value can be used by any command that uses a global
|
||||
vector value from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The vector value calculated by this compute is "extensive." The vector
|
||||
The vector value calculated by this compute is "extensive". The vector
|
||||
value will be in mass\*velocity :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -105,7 +105,7 @@ accessed by indices 1--4 by any command that uses global vector values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values are "intensive." The vector values will be in
|
||||
The vector values are "intensive". The vector values will be in
|
||||
distance\ :math:`^2` :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -121,7 +121,7 @@ These values can be accessed by any command that uses global array values from
|
||||
a compute as input. See the :doc:`Howto output <Howto_output>` page for an
|
||||
overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
distance\ :math:`^2` :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -67,7 +67,7 @@ accessed by indices 1--3 by any command that uses global vector values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values are "intensive." The first vector value will be in
|
||||
The vector values are "intensive". The first vector value will be in
|
||||
distance\ :math:`^2` :doc:`units <units>`, the second is in
|
||||
distance\ :math:`^4` units, and the third is dimensionless.
|
||||
|
||||
|
||||
@ -84,7 +84,7 @@ These values can be accessed by any command that uses global array
|
||||
values from a compute as input. See the :doc:`Howto output <Howto_output>`
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
velocity/distance :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -27,7 +27,7 @@ Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that calculates the potential energy of the
|
||||
entire system of atoms. The specified group must be "all." See the
|
||||
entire system of atoms. The specified group must be "all". See the
|
||||
:doc:`compute pe/atom <compute_pe_atom>` command if you want per-atom
|
||||
energies. These per-atom values could be summed for a group of atoms
|
||||
via the :doc:`compute reduce <compute_reduce>` command.
|
||||
@ -73,7 +73,7 @@ value can be used by any command that uses a global scalar value from
|
||||
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive." The
|
||||
The scalar value calculated by this compute is "extensive". The
|
||||
scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -73,5 +73,5 @@ none
|
||||
.. _Mitchell:
|
||||
|
||||
**(Mitchell)** Mitchell, "A non-local, ordinary-state-based
|
||||
viscoelasticity model for peridynamics," Sandia National Lab Report,
|
||||
viscoelasticity model for peridynamics", Sandia National Lab Report,
|
||||
8064:1-28 (2011).
|
||||
|
||||
@ -29,7 +29,7 @@ Description
|
||||
"""""""""""
|
||||
|
||||
Define a computation that calculates the pressure of the entire system
|
||||
of atoms. The specified group must be "all." See the
|
||||
of atoms. The specified group must be "all". See the
|
||||
:doc:`compute stress/atom <compute_stress_atom>` command if you want per-atom
|
||||
pressure (stress). These per-atom values could be summed for a group
|
||||
of atoms via the :doc:`compute reduce <compute_reduce>` command.
|
||||
@ -115,7 +115,7 @@ LAMMPS starts up, as if this command were in the input script:
|
||||
compute thermo_press all pressure thermo_temp
|
||||
|
||||
where thermo_temp is the ID of a similarly defined compute of style
|
||||
"temp." See the :doc:`thermo_style <thermo_style>` command for more details.
|
||||
"temp". See the :doc:`thermo_style <thermo_style>` command for more details.
|
||||
|
||||
----------
|
||||
|
||||
@ -137,7 +137,7 @@ The ordering of values in the symmetric pressure tensor is as follows:
|
||||
:math:`p_{xz},` :math:`p_{yz}.`
|
||||
|
||||
The scalar and vector values calculated by this compute are
|
||||
"intensive." The scalar and vector values will be in pressure
|
||||
"intensive". The scalar and vector values will be in pressure
|
||||
:doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -110,7 +110,7 @@ accessed by any command that uses global values from a compute as
|
||||
input. See the :doc:`Howto output <Howto_output>` page for an
|
||||
overview of LAMMPS output options.
|
||||
|
||||
The vector or array values are "intensive." The values will be
|
||||
The vector or array values are "intensive". The values will be
|
||||
unitless or in the units discussed above.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -164,7 +164,7 @@ the type of the bond, from 1 to Nbtypes = # of bond types. The number
|
||||
of bond types is defined in the data file read by the
|
||||
:doc:`read_data <read_data>` command.
|
||||
|
||||
The attributes that start with "a," "d," and "i" refer to similar values
|
||||
The attributes that start with "a", "d", and "i" refer to similar values
|
||||
for :doc:`angles <angle_style>`, :doc:`dihedrals <dihedral_style>`, and
|
||||
:doc:`impropers <improper_style>`.
|
||||
|
||||
|
||||
@ -166,7 +166,7 @@ by any command that uses a global values from a compute as input. See
|
||||
the :doc:`Howto output <Howto_output>` page for an overview of
|
||||
LAMMPS output options.
|
||||
|
||||
The array values calculated by this compute are all "intensive."
|
||||
The array values calculated by this compute are all "intensive".
|
||||
|
||||
The first column of array values will be in distance
|
||||
:doc:`units <units>`. The :math:`g(r)` columns of array values are normalized
|
||||
|
||||
@ -128,7 +128,7 @@ inputs to this fix by using the
|
||||
:doc:`compute property/atom <compute_property_atom>` command and then specifying
|
||||
an input value from that compute.
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. Computes can generate
|
||||
per-atom or local quantities. See the individual
|
||||
:doc:`compute <compute>` page for details. If no bracketed integer
|
||||
@ -139,7 +139,7 @@ compute styles and :doc:`add them to LAMMPS <Modify>`. See the
|
||||
discussion above for how :math:`I` can be specified with a wildcard asterisk
|
||||
to effectively specify multiple values.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been
|
||||
If a value begins with "f\_", a fix ID must follow which has been
|
||||
previously defined in the input script. Fixes can generate per-atom
|
||||
or local quantities. See the individual :doc:`fix <fix>` page for
|
||||
details. Note that some fixes only produce their values on certain
|
||||
@ -152,7 +152,7 @@ is used. Users can also write code for their own fix style and
|
||||
:math:`I` can be specified with a wildcard asterisk to effectively specify
|
||||
multiple values.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has
|
||||
If a value begins with "v\_", a variable name must follow which has
|
||||
been previously defined in the input script. It must be an
|
||||
:doc:`atom-style variable <variable>`. Atom-style variables can
|
||||
reference thermodynamic keywords and various per-atom attributes, or
|
||||
@ -197,7 +197,7 @@ global vector of values, the length of which is equal to the number of
|
||||
inputs specified.
|
||||
|
||||
As discussed below, for the *sum*, *sumabs*, and *sumsq* modes, the value(s)
|
||||
produced by this compute are all "extensive," meaning their value
|
||||
produced by this compute are all "extensive", meaning their value
|
||||
scales linearly with the number of atoms involved. If normalized
|
||||
values are desired, this compute can be accessed by the
|
||||
:doc:`thermo_style custom <thermo_style>` command with
|
||||
@ -218,9 +218,9 @@ compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
All the scalar or vector values calculated by this compute are
|
||||
"intensive," except when the *sum*, *sumabs*, or *sumsq* modes are used on
|
||||
"intensive", except when the *sum*, *sumabs*, or *sumsq* modes are used on
|
||||
per-atom or local vectors, in which case the calculated values are
|
||||
"extensive."
|
||||
"extensive".
|
||||
|
||||
The scalar or vector values will be in whatever :doc:`units <units>` the
|
||||
quantities being reduced are in.
|
||||
|
||||
@ -102,7 +102,7 @@ The commands below can be added to the examples/in.micelle script.
|
||||
|
||||
Imagine a collection of polymer chains or small molecules with
|
||||
hydrophobic end groups. All the hydrophobic (HP) atoms are assigned
|
||||
to a group called "phobic."
|
||||
to a group called "phobic".
|
||||
|
||||
These commands will assign a unique cluster ID to all HP atoms within
|
||||
a specified distance of each other. A cluster will contain all HP
|
||||
|
||||
@ -114,7 +114,7 @@ This array can be output with :doc:`fix ave/time <fix_ave_time>`,
|
||||
compute p all stress/cartesian x 0.1
|
||||
fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
|
||||
|
||||
The values calculated by this compute are "intensive." The stress
|
||||
The values calculated by this compute are "intensive". The stress
|
||||
values will be in pressure :doc:`units <units>`. The number density
|
||||
values are in inverse volume :doc:`units <units>`.
|
||||
|
||||
|
||||
@ -182,7 +182,7 @@ Output info
|
||||
from individual atoms in both groups).
|
||||
|
||||
Both the scalar and vector values calculated by this compute are
|
||||
"extensive."
|
||||
"extensive".
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -91,7 +91,7 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
|
||||
@ -134,8 +134,8 @@ vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -117,8 +117,8 @@ vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
The vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -242,8 +242,8 @@ can be accessed by any command that uses global array values from a
|
||||
compute as input. Again, see the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive." The array values are "intensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive". The array values are "intensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`. The array values
|
||||
|
||||
@ -87,8 +87,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
The vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -101,8 +101,8 @@ vector of length 6 (KE tensor), which can be accessed by indices 1--6.
|
||||
These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -134,7 +134,7 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
|
||||
@ -53,8 +53,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -67,8 +67,8 @@ vector values from a compute as input. See the
|
||||
options.
|
||||
|
||||
Both the scalar value and the first two values of the vector
|
||||
calculated by this compute are "intensive." The other four vector values
|
||||
are "extensive."
|
||||
calculated by this compute are "intensive". The other four vector values
|
||||
are "extensive".
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -88,9 +88,9 @@ thermostatting.
|
||||
Output info
|
||||
"""""""""""
|
||||
|
||||
The scalar value calculated by this compute is "intensive," meaning it
|
||||
The scalar value calculated by this compute is "intensive", meaning it
|
||||
is independent of the number of atoms in the simulation. The vector
|
||||
values are "extensive," meaning they scale with the number of atoms in
|
||||
values are "extensive", meaning they scale with the number of atoms in
|
||||
the simulation.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -94,8 +94,8 @@ vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -183,8 +183,8 @@ vector or array values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive." The array values are "intensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive". The array values are "intensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`. The first column
|
||||
|
||||
@ -106,8 +106,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -99,8 +99,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
The vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -46,8 +46,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -86,8 +86,8 @@ vector values from a compute as input. See the
|
||||
:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -122,8 +122,8 @@ vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS
|
||||
output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
vector values are "extensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`. The
|
||||
vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -125,7 +125,7 @@ value can be used by any command that uses a global scalar value from
|
||||
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "extensive."
|
||||
The scalar value calculated by this compute is "extensive".
|
||||
|
||||
The scalar value will be in energy :doc:`units <units>`.
|
||||
|
||||
|
||||
@ -83,7 +83,7 @@ array values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
force-distance :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -66,7 +66,7 @@ accessed by indices 1--4 by any command that uses global vector values
|
||||
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The vector values are "intensive." The vector values will be in
|
||||
The vector values are "intensive". The vector values will be in
|
||||
velocity\ :math:`^2` :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -69,7 +69,7 @@ each chunk. These values can be accessed by any command that uses global array
|
||||
values from a compute as input. See the :doc:`Howto output <Howto_output>`
|
||||
page for an overview of LAMMPS output options.
|
||||
|
||||
The array values are "intensive." The array values will be in
|
||||
The array values are "intensive". The array values will be in
|
||||
velocity :doc:`units <units>`.
|
||||
|
||||
Restrictions
|
||||
|
||||
@ -134,9 +134,9 @@ These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input.
|
||||
See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output options.
|
||||
|
||||
The scalar value calculated by this compute is "intensive." The
|
||||
first six elements of vector values are "extensive,"
|
||||
and the seventh element of vector values is "intensive."
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
first six elements of vector values are "extensive",
|
||||
and the seventh element of vector values is "intensive".
|
||||
|
||||
The scalar value will be in temperature :doc:`units <units>`.
|
||||
The first six elements of vector values will be in energy :doc:`units <units>`.
|
||||
|
||||
@ -198,7 +198,7 @@ Voronoi volume, the second is the neighbor count, as described above
|
||||
(read above for the output data in case the *occupation* keyword is
|
||||
specified). These values can be accessed by any command that uses
|
||||
per-atom values from a compute as input. See the :doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
|
||||
options. If the *peratom* keyword is set to "no," the per-atom array
|
||||
options. If the *peratom* keyword is set to "no", the per-atom array
|
||||
is still created, but it is not accessible.
|
||||
|
||||
If the *edge_histo* keyword is used, then this compute generates a
|
||||
|
||||
@ -219,7 +219,7 @@ The array can be accessed by any command that uses global values from
|
||||
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
All array values calculated by this compute are "intensive."
|
||||
All array values calculated by this compute are "intensive".
|
||||
|
||||
Restrictions
|
||||
""""""""""""
|
||||
|
||||
@ -95,7 +95,7 @@ typically created via the :doc:`create_box <create_box>` command.
|
||||
Before using this command, a lattice must also be defined using the
|
||||
:doc:`lattice <lattice>` command, unless you specify the *single* style
|
||||
with units = box or the *random* style. For the remainder of this doc
|
||||
page, a created atom or molecule is referred to as a "particle."
|
||||
page, a created atom or molecule is referred to as a "particle".
|
||||
|
||||
If created particles are individual atoms, they are assigned the
|
||||
specified atom *type*, though this can be altered via the *basis*
|
||||
@ -352,7 +352,7 @@ As an example, these commands can be used in a 2d simulation, to
|
||||
create a sinusoidal surface. Note that the surface is "rough" due to
|
||||
individual lattice points being "above" or "below" the mathematical
|
||||
expression for the sinusoidal curve. If a finer lattice were used,
|
||||
the sinusoid would appear to be "smoother." Also note the use of the
|
||||
the sinusoid would appear to be "smoother". Also note the use of the
|
||||
"xlat" and "ylat" :doc:`thermo_style <thermo_style>` keywords, which
|
||||
converts lattice spacings to distance.
|
||||
|
||||
|
||||
233
doc/src/dump.rst
233
doc/src/dump.rst
@ -224,30 +224,29 @@ page for details.
|
||||
|
||||
The *atom/gz*, *cfg/gz*, *custom/gz*, *local/gz*, and *xyz/gz* styles
|
||||
are identical in command syntax to the corresponding styles without
|
||||
"gz," however, they generate compressed files using the zlib
|
||||
"gz", however, they generate compressed files using the zlib
|
||||
library. Thus the filename suffix ".gz" is mandatory. This is an
|
||||
alternative approach to writing compressed files via a pipe, as done
|
||||
by the regular dump styles, which may be required on clusters where
|
||||
the interface to the high-speed network disallows using the fork()
|
||||
library call (which is needed for a pipe). For the remainder of this
|
||||
page, you should thus consider the *atom* and *atom/gz* styles
|
||||
(etc.) to be inter-changeable, with the exception of the required
|
||||
filename suffix.
|
||||
alternative approach to writing compressed files via a pipe, as done by
|
||||
the regular dump styles, which may be required on clusters where the
|
||||
interface to the high-speed network disallows using the fork() library
|
||||
call (which is needed for a pipe). For the remainder of this page, you
|
||||
should thus consider the *atom* and *atom/gz* styles (etc.) to be
|
||||
inter-changeable, with the exception of the required filename suffix.
|
||||
|
||||
Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*,
|
||||
and *xyz/zstd* styles are identical to the gz styles, but use the Zstd
|
||||
Similarly, the *atom/zstd*, *cfg/zstd*, *custom/zstd*, *local/zstd*, and
|
||||
*xyz/zstd* styles are identical to the gz styles, but use the Zstd
|
||||
compression library instead and require the ".zst" suffix. See the
|
||||
:doc:`dump_modify <dump_modify>` page for details on how to control
|
||||
the compression level in both variants.
|
||||
:doc:`dump_modify <dump_modify>` page for details on how to control the
|
||||
compression level in both variants.
|
||||
|
||||
As explained below, the *atom/mpiio*, *cfg/mpiio*, *custom/mpiio*, and
|
||||
*xyz/mpiio* styles are identical in command syntax and in the format
|
||||
of the dump files they create, to the corresponding styles without
|
||||
"mpiio," except the single dump file they produce is written in
|
||||
parallel via the MPI-IO library. For the remainder of this page,
|
||||
you should thus consider the *atom* and *atom/mpiio* styles (etc.) to
|
||||
be inter-changeable. The one exception is how the filename is
|
||||
specified for the MPI-IO styles, as explained below.
|
||||
*xyz/mpiio* styles are identical in command syntax and in the format of
|
||||
the dump files they create, to the corresponding styles without "mpiio",
|
||||
except the single dump file they produce is written in parallel via the
|
||||
MPI-IO library. For the remainder of this page, you should thus
|
||||
consider the *atom* and *atom/mpiio* styles (etc.) to be
|
||||
inter-changeable. The one exception is how the filename is specified
|
||||
for the MPI-IO styles, as explained below.
|
||||
|
||||
.. warning::
|
||||
|
||||
@ -434,7 +433,7 @@ Below is an example for a YAML format dump created by the following commands.
|
||||
dump out all yaml 100 dump.yaml id type x y z vx vy vz ix iy iz
|
||||
dump_modify out time yes units yes thermo yes format 1 %5d format "% 10.6e"
|
||||
|
||||
The tags "time," "units," and "thermo" are optional and enabled by the
|
||||
The tags "time", "units", and "thermo" are optional and enabled by the
|
||||
dump_modify command. The list under the "box" tag has three lines for
|
||||
orthogonal boxes and four lines for triclinic boxes, where the first three are
|
||||
the box boundaries and the fourth the three tilt factors (:math:`xy`,
|
||||
@ -553,15 +552,14 @@ package installed, viz.,
|
||||
make yes-mpiio # installs the MPIIO package
|
||||
make mpi # build LAMMPS for your platform
|
||||
|
||||
Second, use a dump filename which contains ".mpiio." Note that it
|
||||
does not have to end in ".mpiio," just contain those characters.
|
||||
Unlike MPI-IO restart files, which must be both written and read using
|
||||
MPI-IO, the dump files produced by these MPI-IO styles are identical
|
||||
in format to the files produced by their non-MPI-IO style
|
||||
counterparts. This means you can write a dump file using MPI-IO and
|
||||
use the :doc:`read_dump <read_dump>` command or perform other
|
||||
post-processing, just as if the dump file was not written using
|
||||
MPI-IO.
|
||||
Second, use a dump filename which contains ".mpiio". Note that it does
|
||||
not have to end in ".mpiio", just contain those characters. Unlike
|
||||
MPI-IO restart files, which must be both written and read using MPI-IO,
|
||||
the dump files produced by these MPI-IO styles are identical in format
|
||||
to the files produced by their non-MPI-IO style counterparts. This
|
||||
means you can write a dump file using MPI-IO and use the :doc:`read_dump
|
||||
<read_dump>` command or perform other post-processing, just as if the
|
||||
dump file was not written using MPI-IO.
|
||||
|
||||
.. warning::
|
||||
|
||||
@ -570,37 +568,40 @@ MPI-IO.
|
||||
|
||||
Note that MPI-IO dump files are one large file which all processors
|
||||
write to. You thus cannot use the "%" wildcard character described
|
||||
above in the filename since that specifies generation of multiple
|
||||
files. You can use the ".bin" or ".lammpsbin" suffix described below in an
|
||||
MPI-IO dump file; again this file will be written in parallel and have the
|
||||
same binary format as if it were written without MPI-IO.
|
||||
above in the filename since that specifies generation of multiple files.
|
||||
You can use the ".bin" or ".lammpsbin" suffix described below in an
|
||||
MPI-IO dump file; again this file will be written in parallel and have
|
||||
the same binary format as if it were written without MPI-IO.
|
||||
|
||||
If the filename ends with ".bin" or ".lammpsbin," the dump file (or files, if
|
||||
"\*" or "%" is also used) is written in binary format. A binary dump file
|
||||
will be about the same size as a text version, but will typically
|
||||
write out much faster. Of course, when post-processing, you will need
|
||||
to convert it back to text format (see the :ref:`binary2txt tool <binary>`) or
|
||||
write your own code to read the binary file. The format of the binary file can
|
||||
be understood by looking at the :file:`tools/binary2txt.cpp` file. This option
|
||||
is only available for the *atom* and *custom* styles.
|
||||
If the filename ends with ".bin" or ".lammpsbin", the dump file (or
|
||||
files, if "\*" or "%" is also used) is written in binary format. A
|
||||
binary dump file will be about the same size as a text version, but will
|
||||
typically write out much faster. Of course, when post-processing, you
|
||||
will need to convert it back to text format (see the :ref:`binary2txt
|
||||
tool <binary>`) or write your own code to read the binary file. The
|
||||
format of the binary file can be understood by looking at the
|
||||
:file:`tools/binary2txt.cpp` file. This option is only available for
|
||||
the *atom* and *custom* styles.
|
||||
|
||||
If the filename ends with ".gz," the dump file (or files, if "\*" or "%"
|
||||
is also used) is written in gzipped format. A gzipped dump file will be about
|
||||
:math:`3\times` smaller than the text version, but will also take longer
|
||||
to write. This option is not available for the *dcd* and *xtc* styles.
|
||||
If the filename ends with ".gz", the dump file (or files, if "\*" or "%"
|
||||
is also used) is written in gzipped format. A gzipped dump file will be
|
||||
about :math:`3\times` smaller than the text version, but will also take
|
||||
longer to write. This option is not available for the *dcd* and *xtc*
|
||||
styles.
|
||||
|
||||
----------
|
||||
|
||||
Note that in the discussion which follows, for styles which can
|
||||
reference values from a compute or fix or custom atom property, like
|
||||
the *custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i` can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form "\*" or "\*n" or "m\*"
|
||||
or "m\*n." If :math:`N` is the number of columns in the array, then an
|
||||
asterisk with no numeric values means all column indices from 1 to :math:`N`.
|
||||
A leading asterisk means all indices from 1 to n (inclusive). A
|
||||
trailing asterisk means all indices from m to :math:`N` (inclusive). A middle
|
||||
asterisk means all indices from m to n (inclusive).
|
||||
reference values from a compute or fix or custom atom property, like the
|
||||
*custom*\ , *cfg*\ , or *local* styles, the bracketed index :math:`i`
|
||||
can be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
|
||||
"m\*n". If :math:`N` is the number of columns in the array, then an
|
||||
asterisk with no numeric values means all column indices from 1 to
|
||||
:math:`N`. A leading asterisk means all indices from 1 to n
|
||||
(inclusive). A trailing asterisk means all indices from m to :math:`N`
|
||||
(inclusive). A middle asterisk means all indices from m to n
|
||||
(inclusive).
|
||||
|
||||
Using a wildcard is the same as if the individual columns of the array
|
||||
had been listed one by one. For example, these two dump commands are
|
||||
@ -679,37 +680,38 @@ The *id*, *mol*, *proc*, *procp1*, *type*, *element*, *mass*, *vx*,
|
||||
|
||||
*Id* is the atom ID. *Mol* is the molecule ID, included in the data
|
||||
file for molecular systems. *Proc* is the ID of the processor (0 to
|
||||
:math:`N_\text{procs}-1`) that currently owns the atom.
|
||||
*Procp1* is the proc ID+1, which can be convenient in place of a *type*
|
||||
attribute (1 to :math:`N_\text{types}`) for coloring atoms in a visualization
|
||||
program. *Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is
|
||||
typically the chemical name of an element, which you must assign to each type
|
||||
via the :doc:`dump_modify element <dump_modify>` command. More generally, it
|
||||
can be any string you wish to associated with an atom type. *Mass* is the atom
|
||||
mass. The quantities *vx*, *vy*, *vz*, *fx*, *fy*, *fz*, and *q* are components
|
||||
of atom velocity and force and atomic charge.
|
||||
:math:`N_\text{procs}-1`) that currently owns the atom. *Procp1* is the
|
||||
proc ID+1, which can be convenient in place of a *type* attribute (1 to
|
||||
:math:`N_\text{types}`) for coloring atoms in a visualization program.
|
||||
*Type* is the atom type (1 to :math:`N_\text{types}`). *Element* is
|
||||
typically the chemical name of an element, which you must assign to each
|
||||
type via the :doc:`dump_modify element <dump_modify>` command. More
|
||||
generally, it can be any string you wish to associated with an atom
|
||||
type. *Mass* is the atom mass. The quantities *vx*, *vy*, *vz*, *fx*,
|
||||
*fy*, *fz*, and *q* are components of atom velocity and force and atomic
|
||||
charge.
|
||||
|
||||
There are several options for outputting atom coordinates. The *x*,
|
||||
*y*, and *z* attributes write atom coordinates "unscaled," in the
|
||||
*y*, and *z* attributes write atom coordinates "unscaled", in the
|
||||
appropriate distance :doc:`units <units>` (:math:`\mathrm{\mathring A}`,
|
||||
:math:`\sigma`, etc.). Use *xs*, *ys*, and *zs* if you want the coordinates
|
||||
"scaled" to the box size so that each value is 0.0 to 1.0. If the simulation
|
||||
box is triclinic (tilted), then all atom coords will still be between 0.0 and
|
||||
1.0. The actual unscaled :math:`(x,y,z)` coordinate is
|
||||
:math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are the non-orthogonal
|
||||
vectors of the simulation box edges, as discussed on the
|
||||
:doc:`Howto triclinic <Howto_triclinic>` page.
|
||||
:math:`\sigma`, etc.). Use *xs*, *ys*, and *zs* if you want the
|
||||
coordinates "scaled" to the box size so that each value is 0.0 to 1.0.
|
||||
If the simulation box is triclinic (tilted), then all atom coords will
|
||||
still be between 0.0 and 1.0. The actual unscaled :math:`(x,y,z)`
|
||||
coordinate is :math:`x_s a + y_s b + z_s c`, where :math:`(a,b,c)` are
|
||||
the non-orthogonal vectors of the simulation box edges, as discussed on
|
||||
the :doc:`Howto triclinic <Howto_triclinic>` page.
|
||||
|
||||
Use *xu*, *yu*, and *zu* if you want the coordinates "unwrapped" by the
|
||||
image flags for each atom. Unwrapped means that if the atom has
|
||||
passed through a periodic boundary one or more times, the value is
|
||||
printed for what the coordinate would be if it had not been wrapped
|
||||
back into the periodic box. Note that using *xu*, *yu*, and *zu* means
|
||||
that the coordinate values may be far outside the box bounds printed
|
||||
with the snapshot. Using *xsu*, *ysu*, and *zsu* is similar to using
|
||||
*xu*, *yu*, and *zu*, except that the unwrapped coordinates are scaled by
|
||||
the box size. Atoms that have passed through a periodic boundary will
|
||||
have the corresponding coordinate increased or decreased by 1.0.
|
||||
image flags for each atom. Unwrapped means that if the atom has passed
|
||||
through a periodic boundary one or more times, the value is printed for
|
||||
what the coordinate would be if it had not been wrapped back into the
|
||||
periodic box. Note that using *xu*, *yu*, and *zu* means that the
|
||||
coordinate values may be far outside the box bounds printed with the
|
||||
snapshot. Using *xsu*, *ysu*, and *zsu* is similar to using *xu*, *yu*,
|
||||
and *zu*, except that the unwrapped coordinates are scaled by the box
|
||||
size. Atoms that have passed through a periodic boundary will have the
|
||||
corresponding coordinate increased or decreased by 1.0.
|
||||
|
||||
The image flags can be printed directly using the *ix*, *iy*, and *iz*
|
||||
attributes. For periodic dimensions, they specify which image of the
|
||||
@ -721,8 +723,8 @@ periodic boundaries during the simulation.
|
||||
|
||||
The *mux*, *muy*, and *muz* attributes are specific to dipolar systems
|
||||
defined with an atom style of *dipole*\ . They give the orientation of
|
||||
the atom's point dipole moment. The *mu* attribute gives the
|
||||
magnitude of the atom's dipole moment.
|
||||
the atom's point dipole moment. The *mu* attribute gives the magnitude
|
||||
of the atom's dipole moment.
|
||||
|
||||
The *radius* and *diameter* attributes are specific to spherical
|
||||
particles that have a finite size, such as those defined with an atom
|
||||
@ -736,17 +738,17 @@ The *angmomx*, *angmomy*, and *angmomz* attributes are specific to
|
||||
finite-size aspherical particles that have an angular momentum. Only
|
||||
the *ellipsoid* atom style defines this quantity.
|
||||
|
||||
The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles that
|
||||
can sustain a rotational torque due to interactions with other
|
||||
The *tqx*, *tqy*, and *tqz* attributes are for finite-size particles
|
||||
that can sustain a rotational torque due to interactions with other
|
||||
particles.
|
||||
|
||||
The *c_ID* and *c_ID[I]* attributes allow per-atom vectors or arrays
|
||||
calculated by a :doc:`compute <compute>` to be output. The ID in the
|
||||
attribute should be replaced by the actual ID of the compute that has
|
||||
been defined previously in the input script. See the
|
||||
:doc:`compute <compute>` command for details. There are computes for
|
||||
calculating the per-atom energy, stress, centro-symmetry parameter,
|
||||
and coordination number of individual atoms.
|
||||
been defined previously in the input script. See the :doc:`compute
|
||||
<compute>` command for details. There are computes for calculating the
|
||||
per-atom energy, stress, centro-symmetry parameter, and coordination
|
||||
number of individual atoms.
|
||||
|
||||
Note that computes which calculate global or local quantities, as
|
||||
opposed to per-atom quantities, cannot be output in a dump custom
|
||||
@ -754,39 +756,39 @@ command. Instead, global quantities can be output by the
|
||||
:doc:`thermo_style custom <thermo_style>` command, and local quantities
|
||||
can be output by the dump local command.
|
||||
|
||||
If *c_ID* is used as a attribute, then the per-atom vector calculated
|
||||
by the compute is printed. If *c_ID[i]* is used, then :math:`i` must be in
|
||||
the range from 1 to :math:`M`, which will print the :math:`i`\ th column of the
|
||||
per-atom array with :math:`M` columns calculated by the compute. See the
|
||||
discussion above for how :math:`i` can be specified with a wildcard asterisk to
|
||||
effectively specify multiple values.
|
||||
If *c_ID* is used as a attribute, then the per-atom vector calculated by
|
||||
the compute is printed. If *c_ID[i]* is used, then :math:`i` must be in
|
||||
the range from 1 to :math:`M`, which will print the :math:`i`\ th column
|
||||
of the per-atom array with :math:`M` columns calculated by the compute.
|
||||
See the discussion above for how :math:`i` can be specified with a
|
||||
wildcard asterisk to effectively specify multiple values.
|
||||
|
||||
The *f_ID* and *f_ID[I]* attributes allow vector or array per-atom
|
||||
quantities calculated by a :doc:`fix <fix>` to be output. The ID in
|
||||
the attribute should be replaced by the actual ID of the fix that has
|
||||
been defined previously in the input script. The :doc:`fix ave/atom
|
||||
quantities calculated by a :doc:`fix <fix>` to be output. The ID in the
|
||||
attribute should be replaced by the actual ID of the fix that has been
|
||||
defined previously in the input script. The :doc:`fix ave/atom
|
||||
<fix_ave_atom>` command is one that calculates per-atom quantities.
|
||||
Since it can time-average per-atom quantities produced by any
|
||||
:doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style
|
||||
:doc:`variable <variable>`, this allows those time-averaged results to
|
||||
be written to a dump file.
|
||||
:doc:`compute <compute>`, :doc:`fix <fix>`, or atom-style :doc:`variable
|
||||
<variable>`, this allows those time-averaged results to be written to a
|
||||
dump file.
|
||||
|
||||
If *f_ID* is used as a attribute, then the per-atom vector calculated
|
||||
by the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the
|
||||
range from 1 to :math:`M`, which will print the :math:`i`\ th column of the
|
||||
per-atom array with :math:`M` columns calculated by the fix. See the
|
||||
discussion above for how :math:`i` can be specified with a wildcard asterisk
|
||||
to effectively specify multiple values.
|
||||
If *f_ID* is used as a attribute, then the per-atom vector calculated by
|
||||
the fix is printed. If *f_ID[i]* is used, then :math:`i` must be in the
|
||||
range from 1 to :math:`M`, which will print the :math:`i`\ th column of
|
||||
the per-atom array with :math:`M` columns calculated by the fix. See
|
||||
the discussion above for how :math:`i` can be specified with a wildcard
|
||||
asterisk to effectively specify multiple values.
|
||||
|
||||
The *v_name* attribute allows per-atom vectors calculated by a
|
||||
:doc:`variable <variable>` to be output. The name in the attribute
|
||||
should be replaced by the actual name of the variable that has been
|
||||
defined previously in the input script. Only an atom-style variable
|
||||
can be referenced, since it is the only style that generates per-atom
|
||||
defined previously in the input script. Only an atom-style variable can
|
||||
be referenced, since it is the only style that generates per-atom
|
||||
values. Variables of style *atom* can reference individual atom
|
||||
attributes, per-atom attributes, thermodynamic keywords, or invoke
|
||||
other computes, fixes, or variables when they are evaluated, so this
|
||||
is a very general means of creating quantities to output to a dump file.
|
||||
attributes, per-atom attributes, thermodynamic keywords, or invoke other
|
||||
computes, fixes, or variables when they are evaluated, so this is a very
|
||||
general means of creating quantities to output to a dump file.
|
||||
|
||||
The *i_name*, *d_name*, *i2_name*, *d2_name* attributes refer to
|
||||
per-atom integer and floating-point vectors or arrays that have been
|
||||
@ -794,10 +796,11 @@ added via the :doc:`fix property/atom <fix_property_atom>` command.
|
||||
When that command is used specific names are given to each attribute
|
||||
which are the "name" portion of these keywords. For arrays *i2_name*
|
||||
and *d2_name*, the column of the array must also be included following
|
||||
the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is in the
|
||||
range from 1 to :math:`M`, where :math:`M` is the number of columns in the
|
||||
custom array). See the discussion above for how :math:`i` can be specified with
|
||||
a wildcard asterisk to effectively specify multiple values.
|
||||
the name in brackets (e.g., d2_xyz[i], i2_mySpin[i], where :math:`i` is
|
||||
in the range from 1 to :math:`M`, where :math:`M` is the number of
|
||||
columns in the custom array). See the discussion above for how :math:`i`
|
||||
can be specified with a wildcard asterisk to effectively specify
|
||||
multiple values.
|
||||
|
||||
See the :doc:`Modify <Modify>` page for information on how to add
|
||||
new compute and fix styles to LAMMPS to calculate per-atom quantities
|
||||
|
||||
@ -196,8 +196,8 @@ Only atoms in the specified group are rendered in the image. The
|
||||
alter what atoms are included in the image.
|
||||
The filename suffix determines whether a JPEG, PNG, or PPM file is
|
||||
created with the *image* dump style. If the suffix is ".jpg" or
|
||||
".jpeg," then a `JPEG format <jpeg_format_>`_ file is created, if the
|
||||
suffix is ".png," then a `PNG format <png_format_>`_ is created, else
|
||||
".jpeg", then a `JPEG format <jpeg_format_>`_ file is created, if the
|
||||
suffix is ".png", then a `PNG format <png_format_>`_ is created, else
|
||||
a `PPM (aka NETPBM) format <ppm_format_>`_ file is created.
|
||||
The JPEG and PNG files are binary; PPM has a text mode header followed
|
||||
by binary data. JPEG images have lossy compression, PNG has lossless
|
||||
@ -261,7 +261,7 @@ atoms rendered in the image. They can be any atom attribute defined
|
||||
for the :doc:`dump custom <dump>` command, including *type* and
|
||||
*element*\ . This includes per-atom quantities calculated by a
|
||||
:doc:`compute <compute>`, :doc:`fix <fix>`, or :doc:`variable <variable>`,
|
||||
which are prefixed by "c\_," "f\_," or "v\_," respectively. Note that the
|
||||
which are prefixed by "c\_", "f\_", or "v\_", respectively. Note that the
|
||||
*diameter* setting can be overridden with a numeric value applied to
|
||||
all atoms by the optional *adiam* keyword.
|
||||
|
||||
@ -297,18 +297,18 @@ and sizes used by the `AtomEye <atomeye_>`_ visualization package.
|
||||
If other atom attributes are used for the *color* or *diameter*
|
||||
settings, they are interpreted in the following way.
|
||||
|
||||
If "vx," for example, is used as the *color* setting, then the color
|
||||
If "vx", for example, is used as the *color* setting, then the color
|
||||
of the atom will depend on the x-component of its velocity. The
|
||||
association of a per-atom value with a specific color is determined by
|
||||
a "color map," which can be specified via the dump_modify command, as
|
||||
a "color map", which can be specified via the dump_modify command, as
|
||||
described below. The basic idea is that the atom-attribute will be
|
||||
within a range of values, and every value within the range is mapped
|
||||
to a specific color. Depending on how the color map is defined, that
|
||||
mapping can take place via interpolation so that a value of -3.2 is
|
||||
halfway between "red" and "blue," or discretely so that the value of
|
||||
halfway between "red" and "blue", or discretely so that the value of
|
||||
-3.2 is "orange".
|
||||
|
||||
If "vx," for example, is used as the *diameter* setting, then the atom
|
||||
If "vx", for example, is used as the *diameter* setting, then the atom
|
||||
will be rendered using the x-component of its velocity as the
|
||||
diameter. If the per-atom value <= 0.0, them the atom will not be
|
||||
drawn. Note that finite-size spherical particles, as defined by
|
||||
@ -792,14 +792,14 @@ increasing values. Note that numeric values can be specified either
|
||||
as absolute numbers or as fractions (0.0 to 1.0) of the range,
|
||||
depending on the "a" or "f" in the style setting for the color map.
|
||||
|
||||
Here is how the entries are used to determine the color of an
|
||||
individual atom, given the value :math:`X` of its atom attribute.
|
||||
:math:`X` will fall between 2 of the entry values. The color of the atom is
|
||||
linearly interpolated (in each of the RGB values) between the 2 colors
|
||||
associated with those entries. For example, if :math:`X = -5.0` and the two
|
||||
surrounding entries are "red" at :math:`-10.0` and "blue" at :math:`0.0`,
|
||||
then the atom's color will be halfway between "red" and "blue," which happens
|
||||
to be "purple."
|
||||
Here is how the entries are used to determine the color of an individual
|
||||
atom, given the value :math:`X` of its atom attribute. :math:`X` will
|
||||
fall between 2 of the entry values. The color of the atom is linearly
|
||||
interpolated (in each of the RGB values) between the 2 colors associated
|
||||
with those entries. For example, if :math:`X = -5.0` and the two
|
||||
surrounding entries are "red" at :math:`-10.0` and "blue" at
|
||||
:math:`0.0`, then the atom's color will be halfway between "red" and
|
||||
"blue", which happens to be "purple".
|
||||
|
||||
For discrete color maps, each entry has a *lo* and *hi* value and a
|
||||
*color*\ . The *lo* and *hi* settings are either numbers within the
|
||||
@ -807,19 +807,18 @@ range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo*
|
||||
and *hi* settings of the last entry must be *min* and *max*\ . Other
|
||||
entries can have any *lo* and *hi* values and the sub-ranges of
|
||||
different values can overlap. Note that numeric *lo* and *hi* values
|
||||
can be specified either as absolute numbers or as fractions (0.0 to
|
||||
1.0) of the range, depending on the "a" or "f" in the style setting
|
||||
for the color map.
|
||||
can be specified either as absolute numbers or as fractions (0.0 to 1.0)
|
||||
of the range, depending on the "a" or "f" in the style setting for the
|
||||
color map.
|
||||
|
||||
Here is how the entries are used to determine the color of an
|
||||
individual atom, given the value X of its atom attribute. The entries
|
||||
are scanned from first to last. The first time that *lo* <= X <=
|
||||
*hi*, X is assigned the color associated with that entry. You can
|
||||
think of the last entry as assigning a default color (since it will
|
||||
always be matched by X), and the earlier entries as colors that
|
||||
override the default. Also note that no interpolation of a color RGB
|
||||
is done. All atoms will be drawn with one of the colors in the list
|
||||
of entries.
|
||||
Here is how the entries are used to determine the color of an individual
|
||||
atom, given the value X of its atom attribute. The entries are scanned
|
||||
from first to last. The first time that *lo* <= X <= *hi*, X is
|
||||
assigned the color associated with that entry. You can think of the
|
||||
last entry as assigning a default color (since it will always be matched
|
||||
by X), and the earlier entries as colors that override the default.
|
||||
Also note that no interpolation of a color RGB is done. All atoms will
|
||||
be drawn with one of the colors in the list of entries.
|
||||
|
||||
For sequential color maps, each entry has only a *color*\ . Here is how
|
||||
the entries are used to determine the color of an individual atom,
|
||||
@ -867,7 +866,7 @@ that bonds of each type will be drawn in the image.
|
||||
The specified *type* should be an integer from 1 to :math:`N`, where :math:`N`
|
||||
is the number of bond types. A wildcard asterisk can be used in place of or
|
||||
in conjunction with the *type* argument to specify a range of bond
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N`
|
||||
is the number of bond types, then an asterisk with no numerical values
|
||||
means all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
|
||||
@ -122,7 +122,7 @@ The *pstyle* argument is the name of the pair style. If
|
||||
sub-styles using the same pair style, then *pstyle* should be specified
|
||||
as "style:N", where :math:`N` is which instance of the pair style you wish to
|
||||
adapt (e.g., the first or second). For example, *pstyle* could be
|
||||
specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2." The
|
||||
specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2". The
|
||||
*pparam* argument is the name of the parameter to change. This is the
|
||||
current list of pair styles and parameters that can be varied by this
|
||||
fix. See the doc pages for individual pair styles and their energy
|
||||
@ -245,7 +245,7 @@ the coefficients for the symmetric :math:`J,I` interaction to the same values.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N`
|
||||
is the number of atom types, then an asterisk with no numeric values
|
||||
means all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
@ -260,17 +260,17 @@ values defined (via the :doc:`pair_coeff <pair_coeff>` command) for
|
||||
that sub-style.
|
||||
|
||||
The *v_name* argument for keyword *pair* is the name of an
|
||||
:doc:`equal-style variable <variable>` which will be evaluated each
|
||||
time this fix is invoked to set the parameter to a new value. It
|
||||
should be specified as v_name, where name is the variable name.
|
||||
Equal-style variables can specify formulas with various mathematical
|
||||
functions, and include :doc:`thermo_style <thermo_style>` command
|
||||
keywords for the simulation box parameters and timestep and elapsed
|
||||
time. Thus it is easy to specify parameters that change as a function
|
||||
of time or span consecutive runs in a continuous fashion. For the
|
||||
latter, see the *start* and *stop* keywords of the :doc:`run <run>`
|
||||
command and the *elaplong* keyword of :doc:`thermo_style custom
|
||||
<thermo_style>` for details.
|
||||
:doc:`equal-style variable <variable>` which will be evaluated each time
|
||||
this fix is invoked to set the parameter to a new value. It should be
|
||||
specified as v_name, where name is the variable name. Equal-style
|
||||
variables can specify formulas with various mathematical functions, and
|
||||
include :doc:`thermo_style <thermo_style>` command keywords for the
|
||||
simulation box parameters and timestep and elapsed time. Thus it is
|
||||
easy to specify parameters that change as a function of time or span
|
||||
consecutive runs in a continuous fashion. For the latter, see the
|
||||
*start* and *stop* keywords of the :doc:`run <run>` command and the
|
||||
*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for
|
||||
details.
|
||||
|
||||
For example, these commands would change the prefactor coefficient of
|
||||
the :doc:`pair_style soft <pair_soft>` potential from 10.0 to 30.0 in a
|
||||
@ -288,13 +288,14 @@ a bond coefficient over time, very similar to how the *pair* keyword
|
||||
operates. The only difference is that now a bond coefficient for a
|
||||
given bond type is adapted.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the bond type argument to set the coefficients for multiple bond
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
|
||||
is the number of bond types, then an asterisk with no numeric values
|
||||
means all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
(inclusive). A middle asterisk means all types from m to n (inclusive).
|
||||
A wild-card asterisk can be used in place of or in conjunction with the
|
||||
bond type argument to set the coefficients for multiple bond types.
|
||||
This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is
|
||||
the number of bond types, then an asterisk with no numeric values means
|
||||
all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to
|
||||
:math:`N` (inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
Currently *bond* does not support bond_style hybrid nor bond_style
|
||||
hybrid/overlay as bond styles. The bond styles that currently work
|
||||
@ -323,13 +324,14 @@ an angle coefficient over time, very similar to how the *pair* keyword
|
||||
operates. The only difference is that now an angle coefficient for a
|
||||
given angle type is adapted.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the angle type argument to set the coefficients for multiple angle
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N`
|
||||
is the number of angle types, then an asterisk with no numeric values
|
||||
means all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
(inclusive). A middle asterisk means all types from m to n (inclusive).
|
||||
A wild-card asterisk can be used in place of or in conjunction with the
|
||||
angle type argument to set the coefficients for multiple angle types.
|
||||
This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is
|
||||
the number of angle types, then an asterisk with no numeric values means
|
||||
all types from 1 to :math:`N`. A leading asterisk means all types from
|
||||
1 to n (inclusive). A trailing asterisk means all types from m to
|
||||
:math:`N` (inclusive). A middle asterisk means all types from m to n
|
||||
(inclusive).
|
||||
|
||||
Currently *angle* does not support angle_style hybrid nor angle_style
|
||||
hybrid/overlay as angle styles. The angle styles that currently work
|
||||
|
||||
@ -115,7 +115,7 @@ overrides the parameters.
|
||||
|
||||
The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
|
||||
a sub-style name. For example, *pstyle* could be specified as "soft"
|
||||
or "lubricate." The *pparam* argument is the name of the parameter to
|
||||
or "lubricate". The *pparam* argument is the name of the parameter to
|
||||
change. This is the current list of pair styles and parameters that
|
||||
can be varied by this fix. See the doc pages for individual pair
|
||||
styles and their energy formulas for the meaning of these parameters:
|
||||
@ -209,7 +209,7 @@ the coefficients for the symmetric J,I interaction to the same values.
|
||||
|
||||
A wild-card asterisk can be used in place of or in conjunction with
|
||||
the :math:`I,J` arguments to set the coefficients for multiple pairs of atom
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n." If :math:`N` is
|
||||
types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is
|
||||
the number of atom types, then an asterisk with no numeric values means
|
||||
all types from 1 to :math:`N`. A leading asterisk means all types from 1 to n
|
||||
(inclusive). A trailing asterisk means all types from m to :math:`N`
|
||||
|
||||
@ -153,7 +153,7 @@ which can be accessed by various :doc:`output commands
|
||||
<Howto_output>`. The scalar is the potential energy discussed above.
|
||||
The vector is the total force on the group of atoms before the forces
|
||||
on individual atoms are changed by the fix. The scalar and vector
|
||||
values calculated by this fix are "extensive."
|
||||
values calculated by this fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
@ -75,7 +75,7 @@ accessed by various :doc:`output commands <Howto_output>`. The scalar
|
||||
is the potential energy discussed above. The vector is the total
|
||||
torque on the group of atoms before the forces on individual atoms are
|
||||
changed by the fix. The scalar and vector values calculated by this
|
||||
fix are "extensive."
|
||||
fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
@ -124,7 +124,7 @@ setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar is the potential
|
||||
energy discussed above. The scalar value calculated by this fix is
|
||||
"extensive."
|
||||
"extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
@ -138,7 +138,7 @@ setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar is the potential
|
||||
energy discussed above. The scalar value calculated by this fix is
|
||||
"extensive."
|
||||
"extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command.
|
||||
|
||||
@ -135,7 +135,7 @@ fix are listed below.
|
||||
|
||||
This fix computes a global scalar which can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar is the energy
|
||||
discussed in the previous paragraph. The scalar value is "extensive."
|
||||
discussed in the previous paragraph. The scalar value is "extensive".
|
||||
|
||||
No parameter of this fix can be used with the
|
||||
*start/stop* keywords of the :doc:`run <run>` command. This fix is not
|
||||
|
||||
@ -167,7 +167,7 @@ the following global cumulative quantities:
|
||||
* 1 = swap attempts
|
||||
* 2 = swap accepts
|
||||
|
||||
The vector values calculated by this fix are "extensive."
|
||||
The vector values calculated by this fix are "extensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during
|
||||
|
||||
@ -70,7 +70,7 @@ per-atom vectors.
|
||||
Note that for values from a compute or fix, the bracketed index I can
|
||||
be specified using a wildcard asterisk with the index to effectively
|
||||
specify multiple values. This takes the form "\*" or "\*n" or "m\*" or
|
||||
"m\*n." If :math:`N` is the size of the vector (for *mode* = scalar) or the
|
||||
"m\*n". If :math:`N` is the size of the vector (for *mode* = scalar) or the
|
||||
number of columns in the array (for *mode* = vector), then an asterisk
|
||||
with no numeric values means all indices from 1 to :math:`N`. A leading
|
||||
asterisk means all indices from 1 to n (inclusive). A trailing
|
||||
@ -127,7 +127,7 @@ specifying an input value from that compute.
|
||||
:doc:`compute property/atom <compute_property_atom>`
|
||||
command via its *xu*, *yu*, and *zu* attributes.
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed term containing an index :math:`I` is appended, the
|
||||
@ -137,7 +137,7 @@ used. Users can also write code for their own compute styles and
|
||||
:math:`I` can be specified with a wildcard asterisk to effectively specify
|
||||
multiple values.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been previously
|
||||
If a value begins with "f\_", a fix ID must follow which has been previously
|
||||
defined in the input script. If no bracketed term is appended, the per-atom
|
||||
vector calculated by the fix is used. If a bracketed term containing an index
|
||||
:math:`I` is appended, the :math:`I^\text{th}` column of the per-atom array
|
||||
@ -148,7 +148,7 @@ and :doc:`add them to LAMMPS <Modify>`. See the discussion above for how
|
||||
:math:`I` can be specified with a wildcard asterisk to effectively specify
|
||||
multiple values.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has
|
||||
If a value begins with "v\_", a variable name must follow which has
|
||||
been previously defined in the input script as an
|
||||
:doc:`atom-style variable <variable>`. Variables of style *atom* can reference
|
||||
thermodynamic keywords or invoke other computes, fixes, or variables
|
||||
|
||||
@ -288,7 +288,7 @@ together as one set of atoms to calculate their temperature. The
|
||||
compute allows the center-of-mass velocity of each chunk to be
|
||||
subtracted before calculating the temperature; this fix does not.
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
@ -297,7 +297,7 @@ their own compute styles and :doc:`add them to LAMMPS <Modify>`.
|
||||
See the discussion above for how I can be specified with a wildcard
|
||||
asterisk to effectively specify multiple values.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been
|
||||
If a value begins with "f\_", a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the fix is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
@ -308,7 +308,7 @@ their own fix styles and :doc:`add them to LAMMPS <Modify>`. See the
|
||||
discussion above for how I can be specified with a wildcard asterisk
|
||||
to effectively specify multiple values.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has
|
||||
If a value begins with "v\_", a variable name must follow which has
|
||||
been previously defined in the input script. Variables of style
|
||||
*atom* can reference thermodynamic keywords and various per-atom
|
||||
attributes, or invoke other computes, fixes, or variables when they
|
||||
@ -348,7 +348,7 @@ at each sampling step.
|
||||
|
||||
If the *norm* setting is *none*, a similar computation as for the
|
||||
*sample* setting is done, except the individual "average sample
|
||||
values" are "summed sample values." A summed sample value is simply
|
||||
values" are "summed sample values". A summed sample value is simply
|
||||
the chunk value summed over atoms in the sample, without dividing by
|
||||
the number of atoms in the sample. The output value for the chunk on
|
||||
the :math:`N_\text{freq}` timesteps is the average of the
|
||||
@ -494,21 +494,21 @@ relevant to this fix.
|
||||
|
||||
This fix computes a global array of values which can be accessed by
|
||||
various :doc:`output commands <Howto_output>`. The values can only be
|
||||
accessed on timesteps that are multiples of :math:`N_\text{freq}`, since that
|
||||
is when averaging is performed. The global array has # of rows = the number
|
||||
of chunks :math:`N_\text{chunk}`, as calculated by the specified
|
||||
:doc:`compute chunk/atom <compute_chunk_atom>` command. The # of columns is
|
||||
:math:`M+1+N_\text{values}`, where :math:`M \in \{1,\dotsc,4\}`,
|
||||
depending on whether the optional
|
||||
columns for OrigID and CoordN are used, as explained above. Following
|
||||
the optional columns, the next column contains the count of atoms in
|
||||
the chunk, and the remaining columns are the Nvalue quantities. When
|
||||
the array is accessed with a row :math:`I` that exceeds the current number of
|
||||
chunks, than a 0.0 is returned by the fix instead of an error, since
|
||||
the number of chunks can vary as a simulation runs depending on how
|
||||
that value is computed by the compute chunk/atom command.
|
||||
accessed on timesteps that are multiples of :math:`N_\text{freq}`, since
|
||||
that is when averaging is performed. The global array has # of rows =
|
||||
the number of chunks :math:`N_\text{chunk}`, as calculated by the
|
||||
specified :doc:`compute chunk/atom <compute_chunk_atom>` command. The #
|
||||
of columns is :math:`M+1+N_\text{values}`, where :math:`M \in
|
||||
\{1,\dotsc,4\}`, depending on whether the optional columns for OrigID
|
||||
and CoordN are used, as explained above. Following the optional
|
||||
columns, the next column contains the count of atoms in the chunk, and
|
||||
the remaining columns are the Nvalue quantities. When the array is
|
||||
accessed with a row :math:`I` that exceeds the current number of chunks,
|
||||
than a 0.0 is returned by the fix instead of an error, since the number
|
||||
of chunks can vary as a simulation runs depending on how that value is
|
||||
computed by the compute chunk/atom command.
|
||||
|
||||
The array values calculated by this fix are treated as "intensive,"
|
||||
The array values calculated by this fix are treated as "intensive",
|
||||
since they are typically already normalized by the count of atoms in
|
||||
each chunk.
|
||||
|
||||
|
||||
@ -189,7 +189,7 @@ Also, if the *ave* keyword is set to *one* which is the default, then
|
||||
|
||||
----------
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the global scalar calculated by the compute is used. If a
|
||||
bracketed term is appended, the :math:`I^\text{th}` element of the global
|
||||
@ -206,7 +206,7 @@ or :doc:`fix temp/rescale <fix_temp_rescale>`. See the doc pages for
|
||||
these commands which give the IDs of these computes. Users can also
|
||||
write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been
|
||||
If a value begins with "f\_", a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed term is
|
||||
appended, the global scalar calculated by the fix is used. If a
|
||||
bracketed term is appended, the :math:`I^\text{th}` element of the global
|
||||
@ -219,7 +219,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will
|
||||
result. Users can also write code for their own fix styles and
|
||||
:doc:`add them to LAMMPS <Modify>`.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has been
|
||||
If a value begins with "v\_", a variable name must follow which has been
|
||||
previously defined in the input script. Only equal-style or vector-style
|
||||
variables can be referenced; the latter requires a bracketed term to specify
|
||||
the :math:`I^\text{th}` element of the vector calculated by the variable.
|
||||
|
||||
@ -193,7 +193,7 @@ inputs to this fix by using the
|
||||
:doc:`compute property/atom <compute_property_atom>` command and then
|
||||
specifying an input value from that compute.
|
||||
|
||||
If a value begins with "c\_," a compute ID must follow which has been
|
||||
If a value begins with "c\_", a compute ID must follow which has been
|
||||
previously defined in the input script. If *mode* = scalar, then if
|
||||
no bracketed term is appended, the global scalar calculated by the
|
||||
compute is used. If a bracketed term is appended, the Ith element of
|
||||
@ -215,7 +215,7 @@ these commands which give the IDs of these computes. Users can also
|
||||
write code for their own compute styles and
|
||||
:doc:`add them to LAMMPS <Modify>`.
|
||||
|
||||
If a value begins with "f\_," a fix ID must follow which has been
|
||||
If a value begins with "f\_", a fix ID must follow which has been
|
||||
previously defined in the input script. If *mode* = scalar, then if
|
||||
no bracketed term is appended, the global scalar calculated by the fix
|
||||
is used. If a bracketed term is appended, the Ith element of the
|
||||
@ -232,7 +232,7 @@ which must be compatible with :math:`N_\text{every}`, else an error will
|
||||
result. Users can also write code for their own fix styles and
|
||||
:doc:`add them to LAMMPS <Modify>`.
|
||||
|
||||
If a value begins with "v\_," a variable name must follow which has
|
||||
If a value begins with "v\_", a variable name must follow which has
|
||||
been previously defined in the input script. If *mode* = scalar, then
|
||||
only equal-style or vector-style variables can be used, which both
|
||||
produce global values. In this mode, a vector-style variable requires
|
||||
|
||||
@ -358,11 +358,11 @@ of rows = length of the input vectors and # of columns = number of
|
||||
inputs.
|
||||
|
||||
If the fix produces a scalar or vector, then the scalar and each
|
||||
element of the vector can be either "intensive" or "extensive,"
|
||||
element of the vector can be either "intensive" or "extensive",
|
||||
depending on whether the values contributing to the scalar or vector
|
||||
element are "intensive" or "extensive." If the fix produces an array,
|
||||
element are "intensive" or "extensive". If the fix produces an array,
|
||||
then all elements in the array must be the same, either "intensive" or
|
||||
"extensive." If a compute or fix provides the value being time
|
||||
"extensive". If a compute or fix provides the value being time
|
||||
averaged, then the compute or fix determines whether the value is
|
||||
intensive or extensive; see the page for that compute or fix for
|
||||
further info. Values produced by a variable are treated as intensive.
|
||||
|
||||
@ -361,7 +361,7 @@ The "SQUARES" section lists the node IDs of the four vertices in a
|
||||
rectangle for each processor (1 to 4).
|
||||
|
||||
For a 3d problem, the syntax is similar but with eight vertices listed for
|
||||
each processor instead of four, and "SQUARES" replaced by "CUBES."
|
||||
each processor instead of four, and "SQUARES" replaced by "CUBES".
|
||||
|
||||
----------
|
||||
|
||||
@ -387,7 +387,7 @@ number of particles (or total weight) per processor.
|
||||
|
||||
These quantities can be accessed by various
|
||||
:doc:`output commands <Howto_output>`. The scalar and vector values calculated
|
||||
by this fix are "intensive."
|
||||
by this fix are "intensive".
|
||||
|
||||
No parameter of this fix can be used with the *start/stop* keywords of
|
||||
the :doc:`run <run>` command. This fix is not invoked during
|
||||
|
||||
@ -318,7 +318,7 @@ Restrictions
|
||||
""""""""""""
|
||||
|
||||
There can be no more than 32 groups defined at one time, including
|
||||
"all."
|
||||
"all".
|
||||
|
||||
The parent group of a dynamic group cannot itself be a dynamic group.
|
||||
|
||||
|
||||
@ -981,7 +981,7 @@ In the last example, "new-property.edn" and
|
||||
"/home/mary/marys-kim-properties/dissociation-energy.edn" are the names of files
|
||||
that contain user-defined (local) property definitions.
|
||||
|
||||
A KIM property instance takes the form of a "map," i.e. a set of key-value
|
||||
A KIM property instance takes the form of a "map", i.e. a set of key-value
|
||||
pairs akin to Perl's hash, Python's dictionary, or Java's Hashtable. It
|
||||
consists of a set of property key names, each of which is referred to here by
|
||||
the *key_name* argument, that are defined as part of the relevant KIM Property
|
||||
|
||||
@ -140,4 +140,4 @@ none
|
||||
.. _Ziegler:
|
||||
|
||||
**(Ziegler)** J.F. Ziegler, J. P. Biersack and U. Littmark, "The
|
||||
Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
|
||||
Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
|
||||
|
||||
Reference in New Issue
Block a user