From cc2b6a35652921cfe2f8460ec7942d53ff49b164 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Sep 2022 19:02:46 -0400 Subject: [PATCH] reorder punctuation and quotation characters for clarity --- doc/src/Bibliography.rst | 2 +- doc/src/Packages_details.rst | 2 +- doc/src/Run_options.rst | 2 +- doc/src/Speed_intel.rst | 2 +- doc/src/compute_angmom_chunk.rst | 2 +- doc/src/compute_born_matrix.rst | 2 +- doc/src/compute_com.rst | 2 +- doc/src/compute_com_chunk.rst | 2 +- doc/src/compute_dipole.rst | 2 +- doc/src/compute_dipole_chunk.rst | 2 +- doc/src/compute_erotate_asphere.rst | 2 +- doc/src/compute_erotate_rigid.rst | 2 +- doc/src/compute_erotate_sphere.rst | 2 +- doc/src/compute_event_displace.rst | 4 +- doc/src/compute_fep.rst | 2 +- doc/src/compute_group_group.rst | 2 +- doc/src/compute_gyration.rst | 2 +- doc/src/compute_gyration_shape.rst | 2 +- doc/src/compute_gyration_shape_chunk.rst | 2 +- doc/src/compute_heat_flux.rst | 14 +- doc/src/compute_hma.rst | 2 +- doc/src/compute_inertia_chunk.rst | 2 +- doc/src/compute_ke.rst | 2 +- doc/src/compute_ke_rigid.rst | 2 +- doc/src/compute_momentum.rst | 2 +- doc/src/compute_msd.rst | 2 +- doc/src/compute_msd_chunk.rst | 2 +- doc/src/compute_msd_nongauss.rst | 2 +- doc/src/compute_omega_chunk.rst | 2 +- doc/src/compute_pe.rst | 4 +- doc/src/compute_plasticity_atom.rst | 2 +- doc/src/compute_pressure.rst | 6 +- doc/src/compute_property_chunk.rst | 2 +- doc/src/compute_property_local.rst | 2 +- doc/src/compute_rdf.rst | 2 +- doc/src/compute_reduce.rst | 12 +- doc/src/compute_reduce_chunk.rst | 2 +- doc/src/compute_stress_profile.rst | 2 +- doc/src/compute_tally.rst | 2 +- doc/src/compute_temp.rst | 2 +- doc/src/compute_temp_asphere.rst | 4 +- doc/src/compute_temp_body.rst | 4 +- doc/src/compute_temp_chunk.rst | 4 +- doc/src/compute_temp_com.rst | 4 +- doc/src/compute_temp_cs.rst | 4 +- doc/src/compute_temp_deform.rst | 2 +- doc/src/compute_temp_deform_eff.rst | 4 +- doc/src/compute_temp_drude.rst | 4 +- doc/src/compute_temp_eff.rst | 4 +- doc/src/compute_temp_partial.rst | 4 +- doc/src/compute_temp_profile.rst | 4 +- doc/src/compute_temp_ramp.rst | 4 +- doc/src/compute_temp_region.rst | 4 +- doc/src/compute_temp_region_eff.rst | 4 +- doc/src/compute_temp_rotate.rst | 4 +- doc/src/compute_temp_sphere.rst | 4 +- doc/src/compute_ti.rst | 2 +- doc/src/compute_torque_chunk.rst | 2 +- doc/src/compute_vacf.rst | 2 +- doc/src/compute_vcm_chunk.rst | 2 +- doc/src/compute_viscosity_cos.rst | 6 +- doc/src/compute_voronoi_atom.rst | 2 +- doc/src/compute_xrd.rst | 2 +- doc/src/create_atoms.rst | 4 +- doc/src/dump.rst | 233 ++++++++++++----------- doc/src/dump_image.rst | 55 +++--- doc/src/fix_adapt.rst | 56 +++--- doc/src/fix_adapt_fep.rst | 4 +- doc/src/fix_addforce.rst | 2 +- doc/src/fix_addtorque.rst | 2 +- doc/src/fix_amoeba_bitorsion.rst | 2 +- doc/src/fix_amoeba_pitorsion.rst | 2 +- doc/src/fix_atc.rst | 2 +- doc/src/fix_atom_swap.rst | 2 +- doc/src/fix_ave_atom.rst | 8 +- doc/src/fix_ave_chunk.rst | 36 ++-- doc/src/fix_ave_correlate.rst | 6 +- doc/src/fix_ave_histo.rst | 6 +- doc/src/fix_ave_time.rst | 6 +- doc/src/fix_balance.rst | 4 +- doc/src/group.rst | 2 +- doc/src/kim_commands.rst | 2 +- doc/src/pair_zbl.rst | 2 +- 83 files changed, 315 insertions(+), 311 deletions(-) diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index 9f3591dcde..dff457836c 100644 --- a/doc/src/Bibliography.rst +++ b/doc/src/Bibliography.rst @@ -1373,7 +1373,7 @@ Bibliography Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002). **(Ziegler)** - J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985. + J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985. **(Zimmerman2004)** 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. diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 4e75c5e94a..f89ab00039 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -276,7 +276,7 @@ the barostat as outlined in: N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of -molecular liquids," J. Chem. Phys. 143, 243148 (2015). +molecular liquids", J. Chem. Phys. 143, 243148 (2015). **Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University) diff --git a/doc/src/Run_options.rst b/doc/src/Run_options.rst index d2d7f8c155..f3c7973197 100644 --- a/doc/src/Run_options.rst +++ b/doc/src/Run_options.rst @@ -495,7 +495,7 @@ run: write_dump group-ID dumpstyle dumpfile arg1 arg2 ... Note that the specified restartfile and dumpfile names may contain -wild-card characters ("\*","%") as explained on the +wild-card characters ("\*" or "%") as explained on the :doc:`read_restart ` and :doc:`write_dump ` doc pages. The use of "%" means that a parallel restart file and/or parallel dump file can be read and/or written. Note that a filename diff --git a/doc/src/Speed_intel.rst b/doc/src/Speed_intel.rst index 6526f836b2..2b53af8698 100644 --- a/doc/src/Speed_intel.rst +++ b/doc/src/Speed_intel.rst @@ -536,6 +536,6 @@ supported. References """""""""" -* 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. +* 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. * 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. `_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). * 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. diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index 2e98742772..ba3ec526cf 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -78,7 +78,7 @@ These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`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-velocity-distance :doc:`units `. Restrictions diff --git a/doc/src/compute_born_matrix.rst b/doc/src/compute_born_matrix.rst index 920ae46532..52bed6a357 100644 --- a/doc/src/compute_born_matrix.rst +++ b/doc/src/compute_born_matrix.rst @@ -182,7 +182,7 @@ by any command that uses global values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The array values calculated by this compute are all "extensive." +The array values calculated by this compute are all "extensive". Restrictions """""""""""" diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst index df5373293e..6fa3fda64c 100644 --- a/doc/src/compute_com.rst +++ b/doc/src/compute_com.rst @@ -49,7 +49,7 @@ accessed by indices 1--3 by any command that uses global vector values from a compute as input. See the :doc:`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 :doc:`units `. Restrictions diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst index a2df80d5d8..2556d97b09 100644 --- a/doc/src/compute_com_chunk.rst +++ b/doc/src/compute_com_chunk.rst @@ -77,7 +77,7 @@ values can be accessed by any command that uses global array values from a compute as input. See the :doc:`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 distance :doc:`units `. Restrictions diff --git a/doc/src/compute_dipole.rst b/doc/src/compute_dipole.rst index 7fb4b54fab..95c5e216f0 100644 --- a/doc/src/compute_dipole.rst +++ b/doc/src/compute_dipole.rst @@ -54,7 +54,7 @@ the computed dipole moment and a global vector of length 3 with the dipole vector. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The computed values are "intensive." The array values will be in +The computed values are "intensive". The array values will be in dipole units (i.e., charge :doc:`units ` times distance :doc:`units `). diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index 24e6442a63..504e6f20d0 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -86,7 +86,7 @@ chunk. These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`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 dipole units (i.e., charge :doc:`units ` times distance :doc:`units `). diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index 44415c63cc..35691d8c9a 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -48,7 +48,7 @@ used by any command that uses a global scalar value from a compute as input. See the :doc:`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 `. Restrictions diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst index 1e03a2316c..b1342bf15e 100644 --- a/doc/src/compute_erotate_rigid.rst +++ b/doc/src/compute_erotate_rigid.rst @@ -48,7 +48,7 @@ of all the rigid bodies). This value can be used by any command that uses a global scalar value from a compute as input. See the :doc:`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 `. Restrictions diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index 28b0052b89..aae37277a4 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -44,7 +44,7 @@ used by any command that uses a global scalar value from a compute as input. See the :doc:`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 `. Restrictions diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst index f8911e1224..43881460f4 100644 --- a/doc/src/compute_event_displace.rst +++ b/doc/src/compute_event_displace.rst @@ -40,7 +40,7 @@ further than the threshold distance. If the system is undergoing significant center-of-mass motion, due to thermal motion, an external force, or an initial net momentum, then this compute will not be able to distinguish that motion from - local atom displacements and may generate "false positives." + local atom displacements and may generate "false positives". Output info """"""""""" @@ -50,7 +50,7 @@ used by any command that uses a global scalar value from a compute as input. See the :doc:`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 scalar value will be a 0 or 1 as explained above. Restrictions diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index e2de8d405b..481e4ead91 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -299,7 +299,7 @@ These output results can be used by any command that uses a global scalar or vector from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. For example, the computed values can be averaged using :doc:`fix ave/time `. -The values calculated by this compute are "extensive." +The values calculated by this compute are "extensive". Restrictions """""""""""" diff --git a/doc/src/compute_group_group.rst b/doc/src/compute_group_group.rst index 87e855ae1e..b4eccf959f 100644 --- a/doc/src/compute_group_group.rst +++ b/doc/src/compute_group_group.rst @@ -140,7 +140,7 @@ vector values from a compute as input. See the options. Both the scalar and vector values calculated by this compute are -"extensive." The scalar value will be in energy :doc:`units `. +"extensive". The scalar value will be in energy :doc:`units `. The vector values will be in force :doc:`units `. Restrictions diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index 5610dd1d98..eaefc3abbb 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -69,7 +69,7 @@ vector values from a compute as input. See the :doc:`Howto output `, respectively. Restrictions diff --git a/doc/src/compute_gyration_shape.rst b/doc/src/compute_gyration_shape.rst index 892677b0ba..2cbffbbdf4 100644 --- a/doc/src/compute_gyration_shape.rst +++ b/doc/src/compute_gyration_shape.rst @@ -78,7 +78,7 @@ vector values from a compute as input. See the options. The vector values calculated by this compute are -"intensive." The first five vector values will be in +"intensive". The first five vector values will be in distance\ :math:`2` :doc:`units ` while the sixth one is dimensionless. Restrictions diff --git a/doc/src/compute_gyration_shape_chunk.rst b/doc/src/compute_gyration_shape_chunk.rst index 2bf8c970e9..62a25b05a3 100644 --- a/doc/src/compute_gyration_shape_chunk.rst +++ b/doc/src/compute_gyration_shape_chunk.rst @@ -80,7 +80,7 @@ See the :doc:`Howto output ` page for an overview of LAMMPS output options. The array calculated by this compute is -"intensive." The first five columns will be in +"intensive". The first five columns will be in distance\ :math:`^2` :doc:`units ` while the sixth one is dimensionless. Restrictions diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index 4302ecddb8..b88cb76260 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -142,14 +142,14 @@ command that uses global vector values from a compute as input. See the :doc:`Howto output ` documentation for an overview of LAMMPS output options. -The vector values calculated by this compute are "extensive," meaning +The vector values calculated by this compute are "extensive", meaning they scale with the number of atoms in the simulation. They can be -divided by the appropriate volume to get a flux, which would then be -an "intensive" value, meaning independent of the number of atoms in -the simulation. Note that if the compute is "all," then the -appropriate volume to divide by is the simulation box volume. -However, if a sub-group is used, it should be the volume containing -those atoms. +divided by the appropriate volume to get a flux, which would then be an +"intensive" value, meaning independent of the number of atoms in the +simulation. Note that if the compute group is "all", then the +appropriate volume to divide by is the simulation box volume. However, +if a group with a subset of atoms is used, it should be the volume +containing those atoms. The vector values will be in energy\*velocity :doc:`units `. Once divided by a volume the units will be that of flux, namely diff --git a/doc/src/compute_hma.rst b/doc/src/compute_hma.rst index 8c0c958ae5..4fa4579651 100644 --- a/doc/src/compute_hma.rst +++ b/doc/src/compute_hma.rst @@ -172,7 +172,7 @@ requested as arguments to the command (the potential energy, pressure and/or hea 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 ` 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 `. Restrictions diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index 74f59dd7a7..6569c3965d 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -84,7 +84,7 @@ by any command that uses global array values from a compute as input. See the :doc:`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 `. Restrictions diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst index 4eb07b920c..8a19438640 100644 --- a/doc/src/compute_ke.rst +++ b/doc/src/compute_ke.rst @@ -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 ` 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 `. Restrictions diff --git a/doc/src/compute_ke_rigid.rst b/doc/src/compute_ke_rigid.rst index b3e446daf6..e77cabfeb6 100644 --- a/doc/src/compute_ke_rigid.rst +++ b/doc/src/compute_ke_rigid.rst @@ -48,7 +48,7 @@ global scalar value from a compute as input. See the :doc:`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 `. Restrictions diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst index 59215c889b..d16d220673 100644 --- a/doc/src/compute_momentum.rst +++ b/doc/src/compute_momentum.rst @@ -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 ` 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 `. Restrictions diff --git a/doc/src/compute_msd.rst b/doc/src/compute_msd.rst index 77694ca8fc..bc16a3de6f 100644 --- a/doc/src/compute_msd.rst +++ b/doc/src/compute_msd.rst @@ -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 ` 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 `. Restrictions diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index 6be5196782..584453d76b 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -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 ` 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 `. Restrictions diff --git a/doc/src/compute_msd_nongauss.rst b/doc/src/compute_msd_nongauss.rst index 16c4e0b06c..512437a932 100644 --- a/doc/src/compute_msd_nongauss.rst +++ b/doc/src/compute_msd_nongauss.rst @@ -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 ` 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 `, the second is in distance\ :math:`^4` units, and the third is dimensionless. diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index 8c32d6491e..7eaddff602 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -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 ` 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 `. Restrictions diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index 825fe4cba4..a96bdd249e 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -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 ` command if you want per-atom energies. These per-atom values could be summed for a group of atoms via the :doc:`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 ` 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 `. Restrictions diff --git a/doc/src/compute_plasticity_atom.rst b/doc/src/compute_plasticity_atom.rst index ad0c22dbf5..45d77d228d 100644 --- a/doc/src/compute_plasticity_atom.rst +++ b/doc/src/compute_plasticity_atom.rst @@ -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). diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index c1a9e3d2ec..bf344be270 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -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 ` 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 ` 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 ` command for more details. +"temp". See the :doc:`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 `. Restrictions diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index 6475a4b962..7c06b8d51e 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -110,7 +110,7 @@ accessed by any command that uses global values from a compute as input. See the :doc:`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 diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index 2f74f45bf4..f1234ade09 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -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 ` 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 `, :doc:`dihedrals `, and :doc:`impropers `. diff --git a/doc/src/compute_rdf.rst b/doc/src/compute_rdf.rst index 2ccc03cf8f..e40775c6e0 100644 --- a/doc/src/compute_rdf.rst +++ b/doc/src/compute_rdf.rst @@ -166,7 +166,7 @@ by any command that uses a global values from a compute as input. See the :doc:`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 `. The :math:`g(r)` columns of array values are normalized diff --git a/doc/src/compute_reduce.rst b/doc/src/compute_reduce.rst index b85b2b7dbb..89554ebece 100644 --- a/doc/src/compute_reduce.rst +++ b/doc/src/compute_reduce.rst @@ -128,7 +128,7 @@ inputs to this fix by using the :doc:`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 ` page for details. If no bracketed integer @@ -139,7 +139,7 @@ compute styles and :doc:`add them to LAMMPS `. 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 ` 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 `. 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 ` command with @@ -218,9 +218,9 @@ compute as input. See the :doc:`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 ` the quantities being reduced are in. diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index c988af276f..43fee39cf2 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -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 diff --git a/doc/src/compute_stress_profile.rst b/doc/src/compute_stress_profile.rst index 9761c68b1e..cb4628bd5d 100644 --- a/doc/src/compute_stress_profile.rst +++ b/doc/src/compute_stress_profile.rst @@ -114,7 +114,7 @@ This array can be output with :doc:`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 `. The number density values are in inverse volume :doc:`units `. diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index fd979d19a0..6eff1e186e 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -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 """""""""""" diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index 2e9d4ab362..1d5a62d6f6 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -91,7 +91,7 @@ vector values from a compute as input. See the :doc:`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 `. The diff --git a/doc/src/compute_temp_asphere.rst b/doc/src/compute_temp_asphere.rst index cef8d573c1..cba52a68b4 100644 --- a/doc/src/compute_temp_asphere.rst +++ b/doc/src/compute_temp_asphere.rst @@ -134,8 +134,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_body.rst b/doc/src/compute_temp_body.rst index 42497e34cb..64f5ce9a0f 100644 --- a/doc/src/compute_temp_body.rst +++ b/doc/src/compute_temp_body.rst @@ -117,8 +117,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_chunk.rst b/doc/src/compute_temp_chunk.rst index f3d1a83351..c92b4e36e9 100644 --- a/doc/src/compute_temp_chunk.rst +++ b/doc/src/compute_temp_chunk.rst @@ -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 ` 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 `. The vector values will be in energy :doc:`units `. The array values diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index fde6f701fd..d54fa7dfa6 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -87,8 +87,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_cs.rst b/doc/src/compute_temp_cs.rst index 3c9503cf4f..45de17be89 100644 --- a/doc/src/compute_temp_cs.rst +++ b/doc/src/compute_temp_cs.rst @@ -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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index b2d6b68b17..adf76564a8 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -134,7 +134,7 @@ vector values from a compute as input. See the :doc:`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 `. diff --git a/doc/src/compute_temp_deform_eff.rst b/doc/src/compute_temp_deform_eff.rst index 3dd1225299..83535f4727 100644 --- a/doc/src/compute_temp_deform_eff.rst +++ b/doc/src/compute_temp_deform_eff.rst @@ -53,8 +53,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_drude.rst b/doc/src/compute_temp_drude.rst index 8c50831941..8602bc3589 100644 --- a/doc/src/compute_temp_drude.rst +++ b/doc/src/compute_temp_drude.rst @@ -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 """""""""""" diff --git a/doc/src/compute_temp_eff.rst b/doc/src/compute_temp_eff.rst index c76581fa68..3ec6300ca4 100644 --- a/doc/src/compute_temp_eff.rst +++ b/doc/src/compute_temp_eff.rst @@ -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 diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index 0512311d8f..d5628e0d60 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -94,8 +94,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_profile.rst b/doc/src/compute_temp_profile.rst index 9076a6cb14..566d8cf3fc 100644 --- a/doc/src/compute_temp_profile.rst +++ b/doc/src/compute_temp_profile.rst @@ -183,8 +183,8 @@ vector or array values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. The first column diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 13799874ab..5c18243c23 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -106,8 +106,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index c8a3075771..77954e8898 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -99,8 +99,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_region_eff.rst b/doc/src/compute_temp_region_eff.rst index ebfc35cbe6..b8cd73f4fd 100644 --- a/doc/src/compute_temp_region_eff.rst +++ b/doc/src/compute_temp_region_eff.rst @@ -46,8 +46,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_rotate.rst b/doc/src/compute_temp_rotate.rst index e760a49b00..7c445109a1 100644 --- a/doc/src/compute_temp_rotate.rst +++ b/doc/src/compute_temp_rotate.rst @@ -86,8 +86,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_temp_sphere.rst b/doc/src/compute_temp_sphere.rst index 3f41837013..5c7c73a8d2 100644 --- a/doc/src/compute_temp_sphere.rst +++ b/doc/src/compute_temp_sphere.rst @@ -122,8 +122,8 @@ vector values from a compute as input. See the :doc:`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 `. The vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_ti.rst b/doc/src/compute_ti.rst index a32f0d1b18..f1f2e5d430 100644 --- a/doc/src/compute_ti.rst +++ b/doc/src/compute_ti.rst @@ -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 ` 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 `. diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst index 97c9c127b8..23befe8458 100644 --- a/doc/src/compute_torque_chunk.rst +++ b/doc/src/compute_torque_chunk.rst @@ -83,7 +83,7 @@ array values from a compute as input. See the :doc:`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 `. Restrictions diff --git a/doc/src/compute_vacf.rst b/doc/src/compute_vacf.rst index c94277f43b..704e597e18 100644 --- a/doc/src/compute_vacf.rst +++ b/doc/src/compute_vacf.rst @@ -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 ` 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 `. Restrictions diff --git a/doc/src/compute_vcm_chunk.rst b/doc/src/compute_vcm_chunk.rst index 5579208766..c2960075f0 100644 --- a/doc/src/compute_vcm_chunk.rst +++ b/doc/src/compute_vcm_chunk.rst @@ -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 ` 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 `. Restrictions diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index a3adf3d78b..1bf9bc2588 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -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 ` 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 `. The first six elements of vector values will be in energy :doc:`units `. diff --git a/doc/src/compute_voronoi_atom.rst b/doc/src/compute_voronoi_atom.rst index e1f8de0667..699d3f2aaa 100644 --- a/doc/src/compute_voronoi_atom.rst +++ b/doc/src/compute_voronoi_atom.rst @@ -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 ` 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 diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index 39dc78a314..10ee35496d 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -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 ` 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 """""""""""" diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 489d4fa5d1..c8f94f7d5e 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -95,7 +95,7 @@ typically created via the :doc:`create_box ` command. Before using this command, a lattice must also be defined using the :doc:`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 ` keywords, which converts lattice spacings to distance. diff --git a/doc/src/dump.rst b/doc/src/dump.rst index fc86fbaaed..21b82de4f0 100644 --- a/doc/src/dump.rst +++ b/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 ` page for details on how to control -the compression level in both variants. +:doc:`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 ` 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 +` 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 `) 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 `) 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 ` 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 ` 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 ` (: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 ` 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 ` 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 ` 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 ` 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 +` 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 ` 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 ` 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 ` 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 ` command is one that calculates per-atom quantities. Since it can time-average per-atom quantities produced by any -:doc:`compute `, :doc:`fix `, or atom-style -:doc:`variable `, this allows those time-averaged results to -be written to a dump file. +:doc:`compute `, :doc:`fix `, or atom-style :doc:`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 ` 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 ` 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 ` page for information on how to add new compute and fix styles to LAMMPS to calculate per-atom quantities diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 257f7a87a8..c395f6ef06 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -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 `_ file is created, if the -suffix is ".png," then a `PNG format `_ is created, else +".jpeg", then a `JPEG format `_ file is created, if the +suffix is ".png", then a `PNG format `_ is created, else a `PPM (aka NETPBM) 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 ` command, including *type* and *element*\ . This includes per-atom quantities calculated by a :doc:`compute `, :doc:`fix `, or :doc:`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 `_ 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` diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index a782f32331..a0c9c5edea 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -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 ` command) for that sub-style. The *v_name* argument for keyword *pair* is the name of an -:doc:`equal-style 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 ` 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 ` -command and the *elaplong* keyword of :doc:`thermo_style custom -` for details. +:doc:`equal-style 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 ` 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 ` command and the +*elaplong* keyword of :doc:`thermo_style custom ` for +details. For example, these commands would change the prefactor coefficient of the :doc:`pair_style 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 diff --git a/doc/src/fix_adapt_fep.rst b/doc/src/fix_adapt_fep.rst index 2f8a1a9475..c35986de49 100644 --- a/doc/src/fix_adapt_fep.rst +++ b/doc/src/fix_adapt_fep.rst @@ -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 ` 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` diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index 8734593b58..4e696f709b 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -153,7 +153,7 @@ which can be accessed by various :doc:`output commands `. 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 ` command. diff --git a/doc/src/fix_addtorque.rst b/doc/src/fix_addtorque.rst index e90e70a8d3..be2823afcf 100644 --- a/doc/src/fix_addtorque.rst +++ b/doc/src/fix_addtorque.rst @@ -75,7 +75,7 @@ accessed by various :doc:`output commands `. 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 ` command. diff --git a/doc/src/fix_amoeba_bitorsion.rst b/doc/src/fix_amoeba_bitorsion.rst index ebfcf7ad40..a9abaf19ce 100644 --- a/doc/src/fix_amoeba_bitorsion.rst +++ b/doc/src/fix_amoeba_bitorsion.rst @@ -124,7 +124,7 @@ setting for this fix is :doc:`fix_modify virial yes `. This fix computes a global scalar which can be accessed by various :doc:`output commands `. 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 ` command. diff --git a/doc/src/fix_amoeba_pitorsion.rst b/doc/src/fix_amoeba_pitorsion.rst index e20324fa0d..484c1015c8 100644 --- a/doc/src/fix_amoeba_pitorsion.rst +++ b/doc/src/fix_amoeba_pitorsion.rst @@ -138,7 +138,7 @@ setting for this fix is :doc:`fix_modify virial yes `. This fix computes a global scalar which can be accessed by various :doc:`output commands `. 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 ` command. diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index 0aa91dbc6f..c6bde5dcc4 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -135,7 +135,7 @@ fix are listed below. This fix computes a global scalar which can be accessed by various :doc:`output commands `. 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 ` command. This fix is not diff --git a/doc/src/fix_atom_swap.rst b/doc/src/fix_atom_swap.rst index d6779925a5..0deda8a5f5 100644 --- a/doc/src/fix_atom_swap.rst +++ b/doc/src/fix_atom_swap.rst @@ -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 ` command. This fix is not invoked during diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 711aa653e4..e2ca9bf16e 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -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 ` 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 `. 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 `. Variables of style *atom* can reference thermodynamic keywords or invoke other computes, fixes, or variables diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index a014e587eb..354c8d8e8b 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -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 `. 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 `. 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 `. 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 ` 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 ` 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. diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 82046990e0..1aff749048 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -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 `. 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 `. -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 `. -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. diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 56671c30f5..e915526aa7 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -193,7 +193,7 @@ inputs to this fix by using the :doc:`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 `. -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 `. -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 diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index 782f0850cc..0308ecc92a 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -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. diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 7afb077881..bf4f77ecd9 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -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 `. 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 ` command. This fix is not invoked during diff --git a/doc/src/group.rst b/doc/src/group.rst index 5cdbfb5c13..4f2a18c8a6 100644 --- a/doc/src/group.rst +++ b/doc/src/group.rst @@ -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. diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index a002b539bd..d886fa7dab 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -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 diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index bbf9f6bc29..6c698b23d2 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -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.