diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 1a66545054f..0da940565ce 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1054,8 +1054,8 @@ This package has :ref:`specific installation instructions ` on the * ``lib/gpu/README`` * :doc:`Accelerator packages ` * :doc:`GPU package ` -* :doc:`Section 2.6 -sf gpu ` -* :doc:`Section 2.6 -pk gpu ` +* :doc:`Section 4.2 -sf gpu ` +* :doc:`Section 4.2 -pk gpu ` * :doc:`package gpu ` * :doc:`Commands ` pages (:doc:`pair `, :doc:`kspace `) for styles followed by (g) @@ -1165,8 +1165,8 @@ This package has :ref:`specific installation instructions ` on the :doc:` * ``src/INTEL/README`` * :doc:`Accelerator packages ` * :doc:`INTEL package ` -* :doc:`Section 2.6 -sf intel ` -* :doc:`Section 2.6 -pk intel ` +* :doc:`Section 4.2 -sf intel ` +* :doc:`Section 4.2 -pk intel ` * :doc:`package intel ` * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, :doc:`kspace `) for styles followed by (i) @@ -1302,9 +1302,9 @@ This package has :ref:`specific installation instructions ` on the :doc: * ``lib/kokkos/README`` * :doc:`Accelerator packages ` * :doc:`KOKKOS package ` -* :doc:`Section 2.6 -k on ... ` -* :doc:`Section 2.6 -sf kk ` -* :doc:`Section 2.6 -pk kokkos ` +* :doc:`Section 4.2 -k on ... ` +* :doc:`Section 4.2 -sf kk ` +* :doc:`Section 4.2 -pk kokkos ` * :doc:`package kokkos ` * Search the :doc:`commands ` pages (:doc:`fix `, :doc:`compute `, :doc:`pair `, :doc:`bond, angle, dihedral, improper `, @@ -2203,7 +2203,7 @@ This package has :ref:`specific installation instructions ` on the :doc:`Bu * ``src/OPT``: filenames -> commands * :doc:`Accelerator packages ` * :doc:`OPT package ` -* :doc:`Section 2.6 -sf opt ` +* :doc:`Section 4.2 -sf opt ` * Search the :doc:`pair style ` page for styles followed by (t) * `Benchmarks page `_ of website diff --git a/doc/src/Speed_packages.rst b/doc/src/Speed_packages.rst index 167f746a591..898644626df 100644 --- a/doc/src/Speed_packages.rst +++ b/doc/src/Speed_packages.rst @@ -101,7 +101,7 @@ listed above. +-----------------------------------------------------------+---------------------------------------------+ This is discussed on the :doc:`Packages ` and :doc:`extra -Build info ` doc pages, and its use is illustrated in the +Build info ` doc pages, and its use is illustrated in the individual accelerator sections. Typically these steps only need to be done once, to create an executable that uses one or more accelerator packages. diff --git a/doc/src/angle_zero.rst b/doc/src/angle_zero.rst index c87f686bcb2..d6d4618c20e 100644 --- a/doc/src/angle_zero.rst +++ b/doc/src/angle_zero.rst @@ -47,7 +47,7 @@ going to be used to assign an equilibrium angle, e.g. for use with Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/bond_none.rst b/doc/src/bond_none.rst index b418f5c5034..939b9c3b0bb 100644 --- a/doc/src/bond_none.rst +++ b/doc/src/bond_none.rst @@ -29,7 +29,7 @@ calculate bond statistics, but compute no bond interactions. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/bond_zero.rst b/doc/src/bond_zero.rst index cd18e857ef9..d102042295d 100644 --- a/doc/src/bond_zero.rst +++ b/doc/src/bond_zero.rst @@ -46,7 +46,7 @@ going to be used to assign an equilibrium distance, e.g. for use with Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_angle_local.rst b/doc/src/compute_angle_local.rst index 5bd1692355d..21d7acec297 100644 --- a/doc/src/compute_angle_local.rst +++ b/doc/src/compute_angle_local.rst @@ -138,7 +138,7 @@ be in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_angmom_chunk.rst b/doc/src/compute_angmom_chunk.rst index ba3ec526cfa..4bb018dcf88 100644 --- a/doc/src/compute_angmom_chunk.rst +++ b/doc/src/compute_angmom_chunk.rst @@ -83,7 +83,7 @@ mass-velocity-distance :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_body_local.rst b/doc/src/compute_body_local.rst index 95c8b143309..0d9238259af 100644 --- a/doc/src/compute_body_local.rst +++ b/doc/src/compute_body_local.rst @@ -91,7 +91,7 @@ The :doc:`units ` for output values depend on the body style. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_bond.rst b/doc/src/compute_bond.rst index 82caef8e934..a2b186a1e09 100644 --- a/doc/src/compute_bond.rst +++ b/doc/src/compute_bond.rst @@ -49,7 +49,7 @@ The vector values are "extensive" and will be in energy Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_bond_local.rst b/doc/src/compute_bond_local.rst index 74fe4aa3c6f..817fd7904b6 100644 --- a/doc/src/compute_bond_local.rst +++ b/doc/src/compute_bond_local.rst @@ -20,7 +20,6 @@ Syntax *dist* = bond distance *engpot* = bond potential energy *force* = bond force - *dx*,\ *dy*,\ *dz* = components of pairwise distance *fx*,\ *fy*,\ *fz* = components of bond force *engvib* = bond kinetic energy of vibration @@ -47,9 +46,7 @@ Examples compute 1 all bond/local engpot compute 1 all bond/local dist engpot force - compute 1 all bond/local dist fx fy fz b1 b2 - compute 1 all bond/local dist v_distsq set dist d Description @@ -226,7 +223,7 @@ energy :doc:`units `. The output for *force* will be in force Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_centro_atom.rst b/doc/src/compute_centro_atom.rst index eab8793466e..83ac4dffef8 100644 --- a/doc/src/compute_centro_atom.rst +++ b/doc/src/compute_centro_atom.rst @@ -150,7 +150,7 @@ of 12. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_chunk_spread_atom.rst b/doc/src/compute_chunk_spread_atom.rst index dc80ad9ea96..a0459fa4d9a 100644 --- a/doc/src/compute_chunk_spread_atom.rst +++ b/doc/src/compute_chunk_spread_atom.rst @@ -206,7 +206,7 @@ The vector or array values are "intensive". Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_cna_atom.rst b/doc/src/compute_cna_atom.rst index 33329d88d62..9c702fa849d 100644 --- a/doc/src/compute_cna_atom.rst +++ b/doc/src/compute_cna_atom.rst @@ -94,7 +94,7 @@ above. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst index 6fa3fda64c3..4645135cacc 100644 --- a/doc/src/compute_com.rst +++ b/doc/src/compute_com.rst @@ -54,7 +54,7 @@ distance :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst index 2556d97b093..4945774c85f 100644 --- a/doc/src/compute_com_chunk.rst +++ b/doc/src/compute_com_chunk.rst @@ -82,7 +82,7 @@ distance :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index b8bd29135b3..74485c2d396 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -140,7 +140,7 @@ explained above. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst index 1d987ec12f3..b4d748f15af 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -47,7 +47,7 @@ The vector values are "extensive" and will be in energy Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 77f467721de..30db584be95 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -131,7 +131,7 @@ The output for *phi* will be in degrees. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index a2b1d946aed..a6cec0375ae 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -139,7 +139,7 @@ incremental dump files. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst index 611cd83c012..a789b4e9b0d 100644 --- a/doc/src/compute_erotate_sphere_atom.rst +++ b/doc/src/compute_erotate_sphere_atom.rst @@ -51,7 +51,7 @@ The per-atom vector values will be in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_global_atom.rst b/doc/src/compute_global_atom.rst index b013a6f270e..1267a2311c4 100644 --- a/doc/src/compute_global_atom.rst +++ b/doc/src/compute_global_atom.rst @@ -225,7 +225,7 @@ corresponding input values are in. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_gyration.rst b/doc/src/compute_gyration.rst index eaefc3abbb9..7178857a97c 100644 --- a/doc/src/compute_gyration.rst +++ b/doc/src/compute_gyration.rst @@ -74,7 +74,7 @@ distance\ :math:`^2` :doc:`units `, respectively. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_gyration_chunk.rst b/doc/src/compute_gyration_chunk.rst index e7517cdbcd3..fc5fc98c92e 100644 --- a/doc/src/compute_gyration_chunk.rst +++ b/doc/src/compute_gyration_chunk.rst @@ -115,7 +115,7 @@ represented by the formula above. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_heat_flux.rst b/doc/src/compute_heat_flux.rst index b88cb762608..d8d549717d6 100644 --- a/doc/src/compute_heat_flux.rst +++ b/doc/src/compute_heat_flux.rst @@ -157,7 +157,7 @@ energy/area/time :doc:`units ` Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_improper.rst b/doc/src/compute_improper.rst index 75e944d8d24..5601616ed73 100644 --- a/doc/src/compute_improper.rst +++ b/doc/src/compute_improper.rst @@ -47,7 +47,7 @@ The vector values are "extensive" and will be in energy Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_improper_local.rst b/doc/src/compute_improper_local.rst index 5377b60baaf..c7401747f58 100644 --- a/doc/src/compute_improper_local.rst +++ b/doc/src/compute_improper_local.rst @@ -77,7 +77,7 @@ The output for *chi* will be in degrees. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_inertia_chunk.rst b/doc/src/compute_inertia_chunk.rst index 6569c3965d1..5e18dbcc993 100644 --- a/doc/src/compute_inertia_chunk.rst +++ b/doc/src/compute_inertia_chunk.rst @@ -89,7 +89,7 @@ mass\*distance\ :math:`^2` :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_ke.rst b/doc/src/compute_ke.rst index 8a194386407..1e96488ca24 100644 --- a/doc/src/compute_ke.rst +++ b/doc/src/compute_ke.rst @@ -57,7 +57,7 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_ke_atom.rst b/doc/src/compute_ke_atom.rst index 34a5ab4073d..2c601d39baf 100644 --- a/doc/src/compute_ke_atom.rst +++ b/doc/src/compute_ke_atom.rst @@ -44,7 +44,7 @@ The per-atom vector values will be in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_modify.rst b/doc/src/compute_modify.rst index 028eb8b66da..ba0ee847693 100644 --- a/doc/src/compute_modify.rst +++ b/doc/src/compute_modify.rst @@ -60,7 +60,7 @@ temperature is correctly normalized. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_msd_chunk.rst b/doc/src/compute_msd_chunk.rst index 863be4db358..5b0ceb76788 100644 --- a/doc/src/compute_msd_chunk.rst +++ b/doc/src/compute_msd_chunk.rst @@ -126,7 +126,7 @@ distance\ :math:`^2` :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_omega_chunk.rst b/doc/src/compute_omega_chunk.rst index 7eaddff602c..4a04c21be33 100644 --- a/doc/src/compute_omega_chunk.rst +++ b/doc/src/compute_omega_chunk.rst @@ -89,7 +89,7 @@ velocity/distance :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_pair.rst b/doc/src/compute_pair.rst index 84ea6a803c9..38e7ce9a6ba 100644 --- a/doc/src/compute_pair.rst +++ b/doc/src/compute_pair.rst @@ -88,7 +88,7 @@ the page for the pair style for details. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_pair_local.rst b/doc/src/compute_pair_local.rst index 6c5b0de6cbd..27a5f2a2d7f 100644 --- a/doc/src/compute_pair_local.rst +++ b/doc/src/compute_pair_local.rst @@ -180,7 +180,7 @@ The output for *pN* will be in whatever units the pair style defines. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_pe.rst b/doc/src/compute_pe.rst index a96bdd249e6..865aa4606b8 100644 --- a/doc/src/compute_pe.rst +++ b/doc/src/compute_pe.rst @@ -78,7 +78,7 @@ scalar value will be in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_pressure.rst b/doc/src/compute_pressure.rst index 92dcdb307ac..280344334af 100644 --- a/doc/src/compute_pressure.rst +++ b/doc/src/compute_pressure.rst @@ -143,7 +143,7 @@ The scalar and vector values will be in pressure :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_property_atom.rst b/doc/src/compute_property_atom.rst index 9872153a3c0..8ec7213168a 100644 --- a/doc/src/compute_property_atom.rst +++ b/doc/src/compute_property_atom.rst @@ -215,7 +215,7 @@ are given in rad/THz. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index 9981c6770b4..b76d06c08bc 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -118,7 +118,7 @@ unitless or in the units discussed above. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index db46953f6d4..61a7f450a97 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -189,7 +189,7 @@ specified attribute. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_reduce_chunk.rst b/doc/src/compute_reduce_chunk.rst index eeadd50a974..3474bb5b973 100644 --- a/doc/src/compute_reduce_chunk.rst +++ b/doc/src/compute_reduce_chunk.rst @@ -181,7 +181,7 @@ The vector or array values are "intensive". Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_slice.rst b/doc/src/compute_slice.rst index 0da7c995737..9caa367856c 100644 --- a/doc/src/compute_slice.rst +++ b/doc/src/compute_slice.rst @@ -117,7 +117,7 @@ input quantities are in. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_temp.rst b/doc/src/compute_temp.rst index 2638a1ae111..f0655d693d7 100644 --- a/doc/src/compute_temp.rst +++ b/doc/src/compute_temp.rst @@ -112,7 +112,7 @@ values are in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_temp_com.rst b/doc/src/compute_temp_com.rst index c2044491063..d941b159db0 100644 --- a/doc/src/compute_temp_com.rst +++ b/doc/src/compute_temp_com.rst @@ -109,7 +109,7 @@ values is in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_temp_deform.rst b/doc/src/compute_temp_deform.rst index abeb7041cc6..6cfa1d646ec 100644 --- a/doc/src/compute_temp_deform.rst +++ b/doc/src/compute_temp_deform.rst @@ -152,7 +152,7 @@ values are in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_temp_partial.rst b/doc/src/compute_temp_partial.rst index b6803f2c9cd..ac24539f1f3 100644 --- a/doc/src/compute_temp_partial.rst +++ b/doc/src/compute_temp_partial.rst @@ -100,7 +100,7 @@ values are in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 643ca9d1ddb..073d7fabe64 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -119,7 +119,7 @@ values are in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_temp_region.rst b/doc/src/compute_temp_region.rst index d2fc8a1633c..c1a0962b468 100644 --- a/doc/src/compute_temp_region.rst +++ b/doc/src/compute_temp_region.rst @@ -113,7 +113,7 @@ values are in energy :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_torque_chunk.rst b/doc/src/compute_torque_chunk.rst index 23befe8458f..eead757c3be 100644 --- a/doc/src/compute_torque_chunk.rst +++ b/doc/src/compute_torque_chunk.rst @@ -88,7 +88,7 @@ force-distance :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_vacf.rst b/doc/src/compute_vacf.rst index 72f675360c0..6ad63ec2126 100644 --- a/doc/src/compute_vacf.rst +++ b/doc/src/compute_vacf.rst @@ -71,7 +71,7 @@ velocity\ :math:`^2` :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_vacf_chunk.rst b/doc/src/compute_vacf_chunk.rst index 6ae676edaf0..90e2cfeba95 100644 --- a/doc/src/compute_vacf_chunk.rst +++ b/doc/src/compute_vacf_chunk.rst @@ -111,7 +111,7 @@ distance\ :math:`^2` divided by time\ :math:`^2` :doc:`units `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/compute_viscosity_cos.rst b/doc/src/compute_viscosity_cos.rst index bfc0c03d79d..38900cf39be 100644 --- a/doc/src/compute_viscosity_cos.rst +++ b/doc/src/compute_viscosity_cos.rst @@ -164,7 +164,7 @@ Related commands Default """"""" - none +none ---------- diff --git a/doc/src/dielectric.rst b/doc/src/dielectric.rst index 09bd9ef1cf7..48c24431fad 100644 --- a/doc/src/dielectric.rst +++ b/doc/src/dielectric.rst @@ -32,7 +32,7 @@ details. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/dihedral_none.rst b/doc/src/dihedral_none.rst index 9aba2fac13a..f86d8e107a8 100644 --- a/doc/src/dihedral_none.rst +++ b/doc/src/dihedral_none.rst @@ -29,7 +29,7 @@ calculate dihedral statistics, but compute no dihedral interactions. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 8c741faaf3d..635a740bf9d 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -45,7 +45,7 @@ specified. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/dump.rst b/doc/src/dump.rst index a17357f3377..13667180b32 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -982,7 +982,7 @@ the distance and energy of each bond: .. code-block:: LAMMPS compute 1 all property/local batom1 batom2 btype - compute 2 all bond/local dist eng + compute 2 all bond/local dist engpot dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2] ---------- diff --git a/doc/src/echo.rst b/doc/src/echo.rst index 8846a987c91..a76a68f9eb4 100644 --- a/doc/src/echo.rst +++ b/doc/src/echo.rst @@ -33,7 +33,7 @@ of this command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index b7d7d22642a..014474070c3 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -645,7 +645,7 @@ parameters on the outermost rRESPA level. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_addforce.rst b/doc/src/fix_addforce.rst index b54728cc364..7334eed6ec5 100644 --- a/doc/src/fix_addforce.rst +++ b/doc/src/fix_addforce.rst @@ -182,7 +182,7 @@ the iteration count during the minimization. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_align_self.rst b/doc/src/fix_align_self.rst index f0994d8b5ee..b74328dcd56 100644 --- a/doc/src/fix_align_self.rst +++ b/doc/src/fix_align_self.rst @@ -36,8 +36,10 @@ Description .. versionadded:: 10Dec2025 -Add a torque to each atom in the group due to a self-alignment toward an -intrinsic orientation. The torque is given by : +Add a torque to each atom in the group which accounts for the +reorientation of each particle toward its own velocity, a generic +phenomenon called self-alignment (see :ref:`(Baconnier2025) +`). The torque is given by : .. math:: @@ -49,8 +51,7 @@ of the particle, and :math:`\mathbf{v}_i` is its velocity. The self-alignment term, introduced in :ref:`(Shimoyama1996) ` with the study of collective motion in systems of self-propelled particles, is an effective torque arising from -differential drag in asymmetric rigid bodies (see :ref:`(Baconnier2025) -`). +differential drag in asymmetric rigid bodies. For mode *dipole*, :math:`e_i` is just equal to the dipole vectors of @@ -62,11 +63,11 @@ the :math:`e_i` will not be unit vectors. If another command changes the magnitude of the dipole, the applied torque will change accordingly and no warning will be provided by LAMMPS. This is almost never what you want, so ensure you are not - changing dipole magnitudes with another LAMMPS fix or pair - style. Furthermore, self-propulsion forces (almost) always set - :math:`e_i` to be a unit vector for all times, so it's best to set - all the dipole magnitudes to 1.0 unless you have a good reason not to - (see the :doc:`set ` command on how to do this). + changing dipole magnitudes with another LAMMPS fix or pair style. + Furthermore, self-propulsion forces (almost) always set :math:`e_i` + to be a unit vector for all times, so it's best to set all the dipole + magnitudes to 1.0 unless you have a good reason not to (see the + :doc:`set ` command on how to do this). For mode *quat*, :math:`e_i` points in the direction of a unit vector, oriented in the coordinate frame of the ellipsoidal particles, which diff --git a/doc/src/fix_ave_atom.rst b/doc/src/fix_ave_atom.rst index 4105259a394..6a83ecb246c 100644 --- a/doc/src/fix_ave_atom.rst +++ b/doc/src/fix_ave_atom.rst @@ -179,7 +179,7 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_ave_chunk.rst b/doc/src/fix_ave_chunk.rst index 704019d46ae..71d9a68cc6c 100644 --- a/doc/src/fix_ave_chunk.rst +++ b/doc/src/fix_ave_chunk.rst @@ -544,7 +544,7 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_ave_correlate.rst b/doc/src/fix_ave_correlate.rst index 91f5c701aa4..7dbb6be2a27 100644 --- a/doc/src/fix_ave_correlate.rst +++ b/doc/src/fix_ave_correlate.rst @@ -385,7 +385,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_ave_histo.rst b/doc/src/fix_ave_histo.rst index 23775c1f51b..35577f626cb 100644 --- a/doc/src/fix_ave_histo.rst +++ b/doc/src/fix_ave_histo.rst @@ -398,7 +398,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_ave_time.rst b/doc/src/fix_ave_time.rst index c52747e5e18..ef66c2fb4b4 100644 --- a/doc/src/fix_ave_time.rst +++ b/doc/src/fix_ave_time.rst @@ -378,7 +378,7 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_aveforce.rst b/doc/src/fix_aveforce.rst index 36f53ef5710..68d0ee3d219 100644 --- a/doc/src/fix_aveforce.rst +++ b/doc/src/fix_aveforce.rst @@ -97,7 +97,7 @@ the iteration count during the minimization. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_drude_transform.rst b/doc/src/fix_drude_transform.rst index 399bf2dd45a..f24dad2555d 100644 --- a/doc/src/fix_drude_transform.rst +++ b/doc/src/fix_drude_transform.rst @@ -192,7 +192,7 @@ No information about this fix is written to :doc:`binary restart files Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_dt_reset.rst b/doc/src/fix_dt_reset.rst index 03b07776e61..2ec820b0e55 100644 --- a/doc/src/fix_dt_reset.rst +++ b/doc/src/fix_dt_reset.rst @@ -112,7 +112,7 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_enforce2d.rst b/doc/src/fix_enforce2d.rst index 5dd0b79057c..65d4eb449d5 100644 --- a/doc/src/fix_enforce2d.rst +++ b/doc/src/fix_enforce2d.rst @@ -50,7 +50,7 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_external.rst b/doc/src/fix_external.rst index 18ea81c9084..430c102b4df 100644 --- a/doc/src/fix_external.rst +++ b/doc/src/fix_external.rst @@ -203,7 +203,7 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_gravity.rst b/doc/src/fix_gravity.rst index 0590f9cc454..b48dcb6f8d4 100644 --- a/doc/src/fix_gravity.rst +++ b/doc/src/fix_gravity.rst @@ -126,7 +126,7 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_heat.rst b/doc/src/fix_heat.rst index 1badf08bffb..ddd3bcf02e7 100644 --- a/doc/src/fix_heat.rst +++ b/doc/src/fix_heat.rst @@ -126,7 +126,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_indent.rst b/doc/src/fix_indent.rst index 1efdc1fb55e..56d9afc28a0 100644 --- a/doc/src/fix_indent.rst +++ b/doc/src/fix_indent.rst @@ -273,7 +273,7 @@ check if you have done this. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_langevin_drude.rst b/doc/src/fix_langevin_drude.rst index 16a8817d6d1..fca3670aa10 100644 --- a/doc/src/fix_langevin_drude.rst +++ b/doc/src/fix_langevin_drude.rst @@ -280,7 +280,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_langevin_eff.rst b/doc/src/fix_langevin_eff.rst index 21cdc4a7890..64c6296454b 100644 --- a/doc/src/fix_langevin_eff.rst +++ b/doc/src/fix_langevin_eff.rst @@ -102,7 +102,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - none +none This fix is part of the EFF package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. diff --git a/doc/src/fix_lineforce.rst b/doc/src/fix_lineforce.rst index 9b1d30e8322..e3352efa1f8 100644 --- a/doc/src/fix_lineforce.rst +++ b/doc/src/fix_lineforce.rst @@ -46,7 +46,7 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_move.rst b/doc/src/fix_move.rst index a4936781435..c6ceaa8f937 100644 --- a/doc/src/fix_move.rst +++ b/doc/src/fix_move.rst @@ -263,7 +263,7 @@ position and velocity of atoms on the outermost rRESPA level. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_nve.rst b/doc/src/fix_nve.rst index 27eae64cce8..5372e088fcb 100644 --- a/doc/src/fix_nve.rst +++ b/doc/src/fix_nve.rst @@ -58,7 +58,7 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_nve_limit.rst b/doc/src/fix_nve_limit.rst index 3533a63ebc2..b9ec2000c85 100644 --- a/doc/src/fix_nve_limit.rst +++ b/doc/src/fix_nve_limit.rst @@ -90,7 +90,7 @@ the :doc:`run ` command. This fix is not invoked during :doc:`energy minim Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_planeforce.rst b/doc/src/fix_planeforce.rst index f4032cf8294..35a2bf99975 100644 --- a/doc/src/fix_planeforce.rst +++ b/doc/src/fix_planeforce.rst @@ -46,7 +46,7 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_print.rst b/doc/src/fix_print.rst index 1ec643a6354..2df94d02fed 100644 --- a/doc/src/fix_print.rst +++ b/doc/src/fix_print.rst @@ -123,7 +123,7 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_property_atom.rst b/doc/src/fix_property_atom.rst index d20358b7a7a..aef1a6152f6 100644 --- a/doc/src/fix_property_atom.rst +++ b/doc/src/fix_property_atom.rst @@ -330,7 +330,7 @@ minimization `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_restrain.rst b/doc/src/fix_restrain.rst index 1c70793bdc8..568c31dd630 100644 --- a/doc/src/fix_restrain.rst +++ b/doc/src/fix_restrain.rst @@ -257,7 +257,7 @@ the :doc:`run ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_rx.rst b/doc/src/fix_rx.rst index 631b227449b..5afa27e733f 100644 --- a/doc/src/fix_rx.rst +++ b/doc/src/fix_rx.rst @@ -112,7 +112,7 @@ this file is described below. There is no restriction on the total number or reaction equations that are specified. The species names are arbitrary string names that are associated with the species concentrations. Each species in a given -reaction must be preceded by it's stoichiometric coefficient. The +reaction must be preceded by its stoichiometric coefficient. The only delimiters that are recognized between the species are either a *+* or *=* character. The *=* character corresponds to an irreversible reaction. After specifying the reaction, the reaction diff --git a/doc/src/fix_spring.rst b/doc/src/fix_spring.rst index b85fe26813e..8a79a2e807c 100644 --- a/doc/src/fix_spring.rst +++ b/doc/src/fix_spring.rst @@ -145,7 +145,7 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_spring_chunk.rst b/doc/src/fix_spring_chunk.rst index 63a225e8783..0620d995630 100644 --- a/doc/src/fix_spring_chunk.rst +++ b/doc/src/fix_spring_chunk.rst @@ -93,7 +93,7 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_store_force.rst b/doc/src/fix_store_force.rst index acce05fbf81..1043581734c 100644 --- a/doc/src/fix_store_force.rst +++ b/doc/src/fix_store_force.rst @@ -69,7 +69,7 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_store_state.rst b/doc/src/fix_store_state.rst index fa6ad799e0d..fbca2031819 100644 --- a/doc/src/fix_store_state.rst +++ b/doc/src/fix_store_state.rst @@ -163,7 +163,7 @@ the :doc:`run ` command. This fix is not invoked during Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_temp_rescale.rst b/doc/src/fix_temp_rescale.rst index 2dd21783468..2a0632ea9e0 100644 --- a/doc/src/fix_temp_rescale.rst +++ b/doc/src/fix_temp_rescale.rst @@ -165,7 +165,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_tune_kspace.rst b/doc/src/fix_tune_kspace.rst index 17e0710be8e..e9e35b6be4d 100644 --- a/doc/src/fix_tune_kspace.rst +++ b/doc/src/fix_tune_kspace.rst @@ -56,9 +56,9 @@ inordinate amount of wall time to complete. An N of 100 for most problems seems reasonable. Once an optimal parameter set is found, that set is used for the remainder of the run. -This fix uses heuristics to guide it's selection of parameter sets to test, -but the actual timed results will be used to decide which set to use in the -simulation. +This fix uses heuristics to guide its selection of parameter sets to +test, but the actual timed results will be used to decide which set to +use in the simulation. It is not necessary to discard trajectories produced using sub-optimal parameter sets, or a mix of various parameter sets, since the user-prescribed diff --git a/doc/src/fix_vector.rst b/doc/src/fix_vector.rst index ee925b39b07..5552f755e91 100644 --- a/doc/src/fix_vector.rst +++ b/doc/src/fix_vector.rst @@ -182,7 +182,7 @@ This fix is not invoked during :doc:`energy minimization `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_wall_body_polygon.rst b/doc/src/fix_wall_body_polygon.rst index 504ded6aaf0..51024767664 100644 --- a/doc/src/fix_wall_body_polygon.rst +++ b/doc/src/fix_wall_body_polygon.rst @@ -69,7 +69,7 @@ appended. For the *wiggle* keyword, the wall oscillates sinusoidally, similar to the oscillations of particles which can be specified by the :doc:`fix move ` command. This is useful in packing simulations of particles. The arguments to the *wiggle* keyword specify a dimension -for the motion, as well as it's *amplitude* and *period*\ . Note that +for the motion, as well as its *amplitude* and *period*\ . Note that if the dimension is in the plane of the wall, this is effectively a shearing motion. If the dimension is perpendicular to the wall, it is more of a shaking motion. A *zcylinder* wall can only be wiggled in diff --git a/doc/src/fix_wall_body_polyhedron.rst b/doc/src/fix_wall_body_polyhedron.rst index 86bd35ae021..ab1c40de851 100644 --- a/doc/src/fix_wall_body_polyhedron.rst +++ b/doc/src/fix_wall_body_polyhedron.rst @@ -66,7 +66,7 @@ Optionally, the wall can be moving, if the *wiggle* keyword is appended. For the *wiggle* keyword, the wall oscillates sinusoidally, similar to the oscillations of particles which can be specified by the :doc:`fix move ` command. This is useful in packing simulations of particles. The arguments to the *wiggle* keyword specify a dimension -for the motion, as well as it's *amplitude* and *period*\ . Note that +for the motion, as well as its *amplitude* and *period*\ . Note that if the dimension is in the plane of the wall, this is effectively a shearing motion. If the dimension is perpendicular to the wall, it is more of a shaking motion. diff --git a/doc/src/fix_wall_gran.rst b/doc/src/fix_wall_gran.rst index cf3ccd97766..2dfca7fb3d9 100644 --- a/doc/src/fix_wall_gran.rst +++ b/doc/src/fix_wall_gran.rst @@ -168,7 +168,7 @@ For the *wiggle* keyword, the wall oscillates sinusoidally, similar to the oscillations of particles which can be specified by the :doc:`fix move ` command. This is useful in packing simulations of granular particles. The arguments to the *wiggle* keyword specify a -dimension for the motion, as well as it's *amplitude* and *period*\ . +dimension for the motion, as well as its *amplitude* and *period*\ . Note that if the dimension is in the plane of the wall, this is effectively a shearing motion. If the dimension is perpendicular to the wall, it is more of a shaking motion. diff --git a/doc/src/fix_wall_region.rst b/doc/src/fix_wall_region.rst index 67b9b9cdb2e..ba75755ab0b 100644 --- a/doc/src/fix_wall_region.rst +++ b/doc/src/fix_wall_region.rst @@ -245,7 +245,7 @@ invoked by the :doc:`minimize ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/improper_none.rst b/doc/src/improper_none.rst index bb50eaa1219..4397b3b5cb4 100644 --- a/doc/src/improper_none.rst +++ b/doc/src/improper_none.rst @@ -29,7 +29,7 @@ calculate improper statistics, but compute no improper interactions. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/improper_zero.rst b/doc/src/improper_zero.rst index 193c527b2ae..a657dd63aea 100644 --- a/doc/src/improper_zero.rst +++ b/doc/src/improper_zero.rst @@ -42,7 +42,7 @@ specified. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/label.rst b/doc/src/label.rst index cae1386e907..0328933a9f6 100644 --- a/doc/src/label.rst +++ b/doc/src/label.rst @@ -33,7 +33,7 @@ the :doc:`jump ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index cb6d6debc3d..5e99f8b7449 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -221,7 +221,7 @@ search could not reduce the energy. Even if alpha is non-zero, if the then it is possible the last iteration effectively caused no atom movement and thus the evaluated energy did not change and the minimizer terminated. Said another way, even with non-zero forces, -it's possible the effect of those forces is to move atoms a distance +it is possibly the effect of those forces to move atoms a distance less than machine precision, so that the energy cannot be further reduced. diff --git a/doc/src/neighbor.rst b/doc/src/neighbor.rst index 8ccd1fb50da..33e6e82d12e 100644 --- a/doc/src/neighbor.rst +++ b/doc/src/neighbor.rst @@ -104,7 +104,7 @@ are printed to the screen and log file. See the :doc:`Run output ` Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/pair_soft.rst b/doc/src/pair_soft.rst index 1405cb81015..a85a5e7d226 100644 --- a/doc/src/pair_soft.rst +++ b/doc/src/pair_soft.rst @@ -121,7 +121,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/pair_yukawa.rst b/doc/src/pair_yukawa.rst index 2b832f187a1..7fca2cc7a7a 100644 --- a/doc/src/pair_yukawa.rst +++ b/doc/src/pair_yukawa.rst @@ -85,7 +85,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index 597b00de3ae..3ae5e043750 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -121,7 +121,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/partition.rst b/doc/src/partition.rst index 6b1866d8d8e..2726102e05b 100644 --- a/doc/src/partition.rst +++ b/doc/src/partition.rst @@ -65,7 +65,7 @@ command lays out a 3d grid of processors in each of 2 partitions. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/print.rst b/doc/src/print.rst index f5ba16d8b5f..85447ad51ae 100644 --- a/doc/src/print.rst +++ b/doc/src/print.rst @@ -99,7 +99,7 @@ apply to the screen and logfile of the individual partition. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/quit.rst b/doc/src/quit.rst index 2355fb238bf..fbd7d308a72 100644 --- a/doc/src/quit.rst +++ b/doc/src/quit.rst @@ -41,7 +41,7 @@ returned. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/region.rst b/doc/src/region.rst index a6dc781561b..0b18d02d60b 100644 --- a/doc/src/region.rst +++ b/doc/src/region.rst @@ -117,7 +117,7 @@ details on the *side* keyword below. Normally, regions in LAMMPS are "static", meaning their geometric extent does not change with time. If the *move* or *rotate* keyword is used, as described below, the region becomes "dynamic", meaning -it's location or orientation changes with time. This may be useful, +its location or orientation changes with time. This may be useful, for example, when thermostatting a region, via the compute temp/region command, or when the fix wall/region command uses a region surface as a bounding wall on particle motion, i.e. a rotating container. @@ -182,7 +182,7 @@ not have to be of unit length. The "inside" of the plane is the half-space in the direction of the normal vector; see the discussion of the *side* option below. -For style *prism*, a parallelepiped is defined (it's too hard to spell +For style *prism*, a parallelepiped is defined (it is too hard to spell parallelepiped in an input script!). The parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = diff --git a/doc/src/suffix.rst b/doc/src/suffix.rst index 98bb43a02d1..96dae8576de 100644 --- a/doc/src/suffix.rst +++ b/doc/src/suffix.rst @@ -99,7 +99,7 @@ commands in your input script. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/thermo.rst b/doc/src/thermo.rst index f918810cc23..011116861ef 100644 --- a/doc/src/thermo.rst +++ b/doc/src/thermo.rst @@ -54,7 +54,7 @@ timesteps 0, 10, 20, 30, 100, 200, 300, 1000, 2000, *etc*: Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/timer.rst b/doc/src/timer.rst index 46a67c89b23..ea411c20f38 100644 --- a/doc/src/timer.rst +++ b/doc/src/timer.rst @@ -115,7 +115,7 @@ than desired. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/timestep.rst b/doc/src/timestep.rst index 037b3f86420..6a60baecb49 100644 --- a/doc/src/timestep.rst +++ b/doc/src/timestep.rst @@ -35,7 +35,7 @@ the outer loop (largest) timestep. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/uncompute.rst b/doc/src/uncompute.rst index e65cbb20381..49332521f1c 100644 --- a/doc/src/uncompute.rst +++ b/doc/src/uncompute.rst @@ -29,7 +29,7 @@ via the :doc:`compute_modify ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/undump.rst b/doc/src/undump.rst index 89874457b0b..6e5f21efda3 100644 --- a/doc/src/undump.rst +++ b/doc/src/undump.rst @@ -28,7 +28,7 @@ This closes the file associated with the dump. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/unfix.rst b/doc/src/unfix.rst index aeb640201df..164c8712e5f 100644 --- a/doc/src/unfix.rst +++ b/doc/src/unfix.rst @@ -29,7 +29,7 @@ via the :doc:`fix_modify ` command. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/src/AMOEBA/amoeba_convolution.cpp b/src/AMOEBA/amoeba_convolution.cpp index f9a0e794601..b267cee2686 100644 --- a/src/AMOEBA/amoeba_convolution.cpp +++ b/src/AMOEBA/amoeba_convolution.cpp @@ -65,6 +65,7 @@ AmoebaConvolution::AmoebaConvolution(LAMMPS *lmp, Pair *pair, nz = nz_caller; order = order_caller; which = which_caller; + time_fft = 0.0; flag3d = 1; if (which == POLAR_GRIDC || which == INDUCE_GRIDC) flag3d = 0; diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index 4866db51790..0056728b116 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -1810,17 +1810,13 @@ std::string FixNH::get_thermo_colname(int n) ilen = mpchain; if (n < ilen) { ich = n; - if (ich == 0) return fmt::format("f_{}:PE_etap[{}]",id,n+1); - else return fmt::format("f_{}:PE_etap[{}]",id,n+1); + return fmt::format("f_{}:PE_etap[{}]",id,n+1); } n -= ilen; ilen = mpchain; if (n < ilen) { ich = n; - if (ich == 0) - return fmt::format("f_{}:KE_etap_dot[{}]",id,n+1); - else - return fmt::format("f_{}:KE_etap_dot[{}]",id,n+1); + return fmt::format("f_{}:KE_etap_dot[{}]",id,n+1); } n -= ilen; } diff --git a/src/kspace.cpp b/src/kspace.cpp index 88a9f0a7f82..65a6d4d9d92 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -599,11 +599,11 @@ void KSpace::modify_params(int narg, char **arg) if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"kspace_modify force/disp/kspace", error); accuracy_kspace_6 = utils::numeric(FLERR,arg[iarg+1],false,lmp); iarg += 2; - } else if (strcmp(arg[iarg],"eigtol") == 0) { - if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"kspace_modify eigtol", error); + } else if ((strcmp(arg[iarg],"splittol") == 0) || (strcmp(arg[iarg],"eigtol") == 0)) { + if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"kspace_modify splittol", error); splittol = utils::numeric(FLERR,arg[iarg+1],false,lmp); if (splittol >= 1.0) - error->all(FLERR, iarg+1, "Kspace_modify eigtol value must be smaller than one"); + error->all(FLERR, iarg+1, "Kspace_modify splittol value must be smaller than one"); iarg += 2; } else if (strcmp(arg[iarg],"pressure/scalar") == 0) { if (iarg+2 > narg) utils::missing_cmd_args(FLERR,"kspace_modify pressure/scalar", error); diff --git a/src/region.cpp b/src/region.cpp index 8cd3cd3b234..32ef375ed9e 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -39,6 +39,7 @@ Region::Region(LAMMPS *lmp, int /*narg*/, char **arg) : varshape = 0; xstr = ystr = zstr = tstr = nullptr; dx = dy = dz = 0.0; + theta = 0.0; size_restart = 5; Region::reset_vel(); diff --git a/tools/regression-tests/run_tests.py b/tools/regression-tests/run_tests.py index 577ca211c09..a1642670d1c 100755 --- a/tools/regression-tests/run_tests.py +++ b/tools/regression-tests/run_tests.py @@ -1593,7 +1593,8 @@ def has_markers(inputFileName): input_list=['in.lj'] total_tests = len(input_list) results = [] - stat = iterate(lmp_binary, pwd, input_list, config, results, progress_file_abs) + stat = iterate(lmp_binary, pwd, input_list, config, + results, progress_file_abs, failure_file_abs, walltime_ref, verbose, last_progress) completed_tests = stat['num_completed'] skipped_tests = stat['num_skipped']