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Merge pull request #1828 from lammps/post-patch-tweaks

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minor omissions in recent patch release
This commit is contained in:
Axel Kohlmeyer
2020-01-11 21:00:09 -05:00
committed by GitHub
parent 7ebddb6088 b2c4385661
commit 587fc9d962
19 changed files with 112 additions and 1019 deletions
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2
doc/src/Build_extras.rst
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@ -203,7 +203,7 @@ inside the CMake build directory. If the KIM library is already on
your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
environment variable so that libkim-api can be found.
For using KIM web queries.
For using OpenKIM web queries in LAMMPS.
If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
libcurl calls within the KIM web query display a lot of information about

96
doc/src/Commands_all.rst
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@ -25,26 +25,26 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`atom_style <atom_style>`
* :doc:`balance <balance>`
* :doc:`bond_coeff <bond_coeff>`
* :doc:`bond\_style <bond_style>`
* :doc:`bond\_write <bond_write>`
* :doc:`bond_style <bond_style>`
* :doc:`bond_write <bond_write>`
* :doc:`boundary <boundary>`
* :doc:`box <box>`
* :doc:`change\_box <change_box>`
* :doc:`change_box <change_box>`
* :doc:`clear <clear>`
* :doc:`comm\_modify <comm_modify>`
* :doc:`comm\_style <comm_style>`
* :doc:`comm_modify <comm_modify>`
* :doc:`comm_style <comm_style>`
* :doc:`compute <compute>`
* :doc:`compute\_modify <compute_modify>`
* :doc:`create\_atoms <create_atoms>`
* :doc:`create\_bonds <create_bonds>`
* :doc:`create\_box <create_box>`
* :doc:`delete\_atoms <delete_atoms>`
* :doc:`delete\_bonds <delete_bonds>`
* :doc:`compute_modify <compute_modify>`
* :doc:`create_atoms <create_atoms>`
* :doc:`create_bonds <create_bonds>`
* :doc:`create_box <create_box>`
* :doc:`delete_atoms <delete_atoms>`
* :doc:`delete_bonds <delete_bonds>`
* :doc:`dielectric <dielectric>`
* :doc:`dihedral\_coeff <dihedral_coeff>`
* :doc:`dihedral\_style <dihedral_style>`
* :doc:`dihedral_coeff <dihedral_coeff>`
* :doc:`dihedral_style <dihedral_style>`
* :doc:`dimension <dimension>`
* :doc:`displace\_atoms <displace_atoms>`
* :doc:`displace_atoms <displace_atoms>`
* :doc:`dump <dump>`
* :doc:`dump adios <dump_adios>`
* :doc:`dump image <dump_image>`
@ -52,75 +52,77 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`dump netcdf <dump_netcdf>`
* :doc:`dump netcdf/mpiio <dump_netcdf>`
* :doc:`dump vtk <dump_vtk>`
* :doc:`dump\_modify <dump_modify>`
* :doc:`dynamical\_matrix <dynamical_matrix>`
* :doc:`dump_modify <dump_modify>`
* :doc:`dynamical_matrix <dynamical_matrix>`
* :doc:`echo <echo>`
* :doc:`fix <fix>`
* :doc:`fix\_modify <fix_modify>`
* :doc:`fix_modify <fix_modify>`
* :doc:`group <group>`
* :doc:`group2ndx <group2ndx>`
* :doc:`hyper <hyper>`
* :doc:`if <if>`
* :doc:`improper\_coeff <improper_coeff>`
* :doc:`improper\_style <improper_style>`
* :doc:`improper_coeff <improper_coeff>`
* :doc:`improper_style <improper_style>`
* :doc:`include <include>`
* :doc:`info <info>`
* :doc:`jump <jump>`
* :doc:`kim\_init <kim_commands>`
* :doc:`kim\_interactions <kim_commands>`
* :doc:`kim\_query <kim_commands>`
* :doc:`kspace\_modify <kspace_modify>`
* :doc:`kspace\_style <kspace_style>`
* :doc:`kim_init <kim_commands>`
* :doc:`kim_interactions <kim_commands>`
* :doc:`kim_param <kim_commands>`
* :doc:`kim_query <kim_commands>`
* :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>`
* :doc:`label <label>`
* :doc:`lattice <lattice>`
* :doc:`log <log>`
* :doc:`mass <mass>`
* :doc:`message <message>`
* :doc:`minimize <minimize>`
* :doc:`min\_modify <min_modify>`
* :doc:`min\_style <min_style>`
* :doc:`min\_style spin <min_spin>`
* :doc:`min_modify <min_modify>`
* :doc:`min_style <min_style>`
* :doc:`min_style spin <min_spin>`
* :doc:`molecule <molecule>`
* :doc:`ndx2group <group2ndx>`
* :doc:`neb <neb>`
* :doc:`neb/spin <neb_spin>`
* :doc:`neigh\_modify <neigh_modify>`
* :doc:`neigh_modify <neigh_modify>`
* :doc:`neighbor <neighbor>`
* :doc:`newton <newton>`
* :doc:`next <next>`
* :doc:`package <package>`
* :doc:`pair\_coeff <pair_coeff>`
* :doc:`pair\_modify <pair_modify>`
* :doc:`pair\_write <pair_write>`
* :doc:`pair_coeff <pair_coeff>`
* :doc:`pair_modify <pair_modify>`
* :doc:`pair_write <pair_write>`
* :doc:`partition <partition>`
* :doc:`prd <prd>`
* :doc:`print <print>`
* :doc:`processors <processors>`
* :doc:`python <python>`
* :doc:`quit <quit>`
* :doc:`read\_data <read_data>`
* :doc:`read\_dump <read_dump>`
* :doc:`read\_restart <read_restart>`
* :doc:`read_data <read_data>`
* :doc:`read_dump <read_dump>`
* :doc:`read_restart <read_restart>`
* :doc:`region <region>`
* :doc:`replicate <replicate>`
* :doc:`rerun <rerun>`
* :doc:`reset\_ids <reset_ids>`
* :doc:`reset\_timestep <reset_timestep>`
* :doc:`reset_ids <reset_ids>`
* :doc:`reset_timestep <reset_timestep>`
* :doc:`restart <restart>`
* :doc:`run <run>`
* :doc:`run\_style <run_style>`
* :doc:`run_style <run_style>`
* :doc:`server <server>`
* :doc:`set <set>`
* :doc:`shell <shell>`
* :doc:`special\_bonds <special_bonds>`
* :doc:`special_bonds <special_bonds>`
* :doc:`suffix <suffix>`
* :doc:`tad <tad>`
* :doc:`temper <temper>`
* :doc:`temper/grem <temper_grem>`
* :doc:`temper/npt <temper_npt>`
* :doc:`thermo <thermo>`
* :doc:`thermo\_modify <thermo_modify>`
* :doc:`thermo\_style <thermo_style>`
* :doc:`third\_order <third_order>`
* :doc:`thermo_modify <thermo_modify>`
* :doc:`thermo_style <thermo_style>`
* :doc:`third_order <third_order>`
* :doc:`timer <timer>`
* :doc:`timestep <timestep>`
* :doc:`uncompute <uncompute>`
@ -129,7 +131,11 @@ An alphabetic list of all general LAMMPS commands.
* :doc:`units <units>`
* :doc:`variable <variable>`
* :doc:`velocity <velocity>`
* :doc:`write\_coeff <write_coeff>`
* :doc:`write\_data <write_data>`
* :doc:`write\_dump <write_dump>`
* :doc:`write\_restart <write_restart>`
* :doc:`write_coeff <write_coeff>`
* :doc:`write_data <write_data>`
* :doc:`write_dump <write_dump>`
* :doc:`write_restart <write_restart>`
*
*
*
*

14
doc/src/Commands_bond.rst
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@ -13,7 +13,7 @@
.. _bond:
bond_style potentials
Bond_style potentials
=====================
All LAMMPS :doc:`bond_style <bond_style>` commands. Some styles have
@ -44,16 +44,14 @@ OPT.
* :doc:`nonlinear (o) <bond_nonlinear>`
* :doc:`oxdna/fene <bond_oxdna>`
* :doc:`oxdna2/fene <bond_oxdna>`
* :doc:`oxrna2/fene <bond_oxdna>`
* :doc:`quartic (o) <bond_quartic>`
* :doc:`table (o) <bond_table>`
*
*
---
.. _angle:
angle_style potentials
Angle_style potentials
======================
All LAMMPS :doc:`angle_style <angle_style>` commands. Some styles have
@ -93,11 +91,9 @@ OPT.
* :doc:`table (o) <angle_table>`
*
---
.. _dihedral:
dihedral_style potentials
Dihedral_style potentials
=========================
All LAMMPS :doc:`dihedral_style <dihedral_style>` commands. Some styles
@ -136,7 +132,7 @@ OPT.
.. _improper:
improper_style potentials
Improper_style potentials
=========================
All LAMMPS :doc:`improper\_style <improper_style>` commands. Some styles

16
doc/src/Commands_fix.rst
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@ -105,13 +105,13 @@ OPT.
* :doc:`mvv/edpd <fix_mvv_dpd>`
* :doc:`mvv/tdpd <fix_mvv_dpd>`
* :doc:`neb <fix_neb>`
* :doc:`neb\_spin <fix_neb_spin>`
* :doc:`neb/spin <fix_neb_spin>`
* :doc:`nph (ko) <fix_nh>`
* :doc:`nph/asphere (o) <fix_nph_asphere>`
* :doc:`nph/body <fix_nph_body>`
* :doc:`nph/eff <fix_nh_eff>`
* :doc:`nph/sphere (o) <fix_nph_sphere>`
* :doc:`nphug (o) <fix_nphug>`
* :doc:`nphug <fix_nphug>`
* :doc:`npt (iko) <fix_nh>`
* :doc:`npt/asphere (o) <fix_npt_asphere>`
* :doc:`npt/body <fix_npt_body>`
@ -188,15 +188,16 @@ OPT.
* :doc:`rx (k) <fix_rx>`
* :doc:`saed/vtk <fix_saed_vtk>`
* :doc:`setforce (k) <fix_setforce>`
* :doc:`setforce/spin <fix_setforce>`
* :doc:`shake <fix_shake>`
* :doc:`shardlow (k) <fix_shardlow>`
* :doc:`smd <fix_smd>`
* :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`
* :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>`
* :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`
* :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>`
* :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>`
* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>`
* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
* :doc:`smd/setvel <fix_smd_setvel>`
* :doc:`smd/wall\_surface <fix_smd_wall_surface>`
* :doc:`smd/wall_surface <fix_smd_wall_surface>`
* :doc:`spring <fix_spring>`
* :doc:`spring/chunk <fix_spring_chunk>`
* :doc:`spring/rg <fix_spring_rg>`
@ -237,4 +238,3 @@ OPT.
* :doc:`wall/region/ees <fix_wall_ees>`
* :doc:`wall/srd <fix_wall_srd>`
*
*

10
doc/src/Commands_kspace.rst
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@ -24,12 +24,16 @@ OPT.
* :doc:`ewald (o) <kspace_style>`
* :doc:`ewald/disp <kspace_style>`
* :doc:`ewald/dipole <kspace_style>`
* :doc:`ewald/dipole/spin <kspace_style>`
* :doc:`msm (o) <kspace_style>`
* :doc:`msm/cg (o) <kspace_style>`
* :doc:`pppm (gok) <kspace_style>`
* :doc:`pppm (giko) <kspace_style>`
* :doc:`pppm/cg (o) <kspace_style>`
* :doc:`pppm/disp (i) <kspace_style>`
* :doc:`pppm/disp/tip4p <kspace_style>`
* :doc:`pppm/dipole <kspace_style>`
* :doc:`pppm/dipole/spin <kspace_style>`
* :doc:`pppm/disp (io) <kspace_style>`
* :doc:`pppm/disp/tip4p (o) <kspace_style>`
* :doc:`pppm/stagger <kspace_style>`
* :doc:`pppm/tip4p (o) <kspace_style>`
* :doc:`scafacos <kspace_style>`

18
doc/src/Commands_pair.rst
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@ -11,10 +11,10 @@
* :ref:`Improper styles <improper>`
* :doc:`KSpace styles <Commands_kspace>`
Pair\_style potentials
Pair_style potentials
======================
All LAMMPS :doc:`pair\_style <pair_style>` commands. Some styles have
All LAMMPS :doc:`pair_style <pair_style>` commands. Some styles have
accelerated versions. This is indicated by additional letters in
parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
OPT.
@ -146,7 +146,7 @@ OPT.
* :doc:`lj/cut/soft (o) <pair_fep_soft>`
* :doc:`lj/cut/thole/long (o) <pair_thole>`
* :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
* :doc:`lj/cut/tip4p/long (ot) <pair_lj>`
* :doc:`lj/cut/tip4p/long (got) <pair_lj>`
* :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
* :doc:`lj/expand (gko) <pair_lj_expand>`
* :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
@ -162,7 +162,7 @@ OPT.
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (o) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* :doc:`lj96/cut (go) <pair_lj96>`
* :doc:`local/density <pair_local_density>`
* :doc:`lubricate (o) <pair_lubricate>`
@ -176,6 +176,7 @@ OPT.
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
* :doc:`mgpt <pair_mgpt>`
* :doc:`mie/cut (g) <pair_mie>`
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`momb <pair_momb>`
* :doc:`morse (gkot) <pair_morse>`
* :doc:`morse/smooth/linear (o) <pair_morse>`
@ -197,10 +198,17 @@ OPT.
* :doc:`oxdna2/hbond <pair_oxdna2>`
* :doc:`oxdna2/stk <pair_oxdna2>`
* :doc:`oxdna2/xstk <pair_oxdna2>`
* :doc:`oxrna2/excv <pair_oxrna2>`
* :doc:`oxrna2/hbond <pair_oxrna2>`
* :doc:`oxrna2/dh <pair_oxrna2>`
* :doc:`oxrna2/stk <pair_oxrna2>`
* :doc:`oxrna2/xstk <pair_oxrna2>`
* :doc:`oxrna2/coaxstk <pair_oxrna2>`
* :doc:`peri/eps <pair_peri>`
* :doc:`peri/lps (o) <pair_peri>`
* :doc:`peri/pmb (o) <pair_peri>`
* :doc:`peri/ves <pair_peri>`
* :doc:`polymorphic <pair_polymorphic>`
* :doc:`python <pair_python>`
* :doc:`quip <pair_quip>`
* :doc:`reax/c (ko) <pair_reaxc>`
@ -209,7 +217,7 @@ OPT.
* :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
* :doc:`smd/hertz <pair_smd_hertz>`
* :doc:`smd/tlsph <pair_smd_tlsph>`
* :doc:`smd/tri\_surface <pair_smd_triangulated_surface>`
* :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
* :doc:`smd/ulsph <pair_smd_ulsph>`
* :doc:`smtbq <pair_smtbq>`
* :doc:`snap (k) <pair_snap>`

4
doc/src/Packages_details.rst
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@ -2438,8 +2438,8 @@ which discuss the `QuickFF <quickff_>`_ methodology.
* :doc:`bond\_style mm3 <bond_mm3>`
* :doc:`improper\_style distharm <improper_distharm>`
* :doc:`improper\_style sqdistharm <improper_sqdistharm>`
* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss>`
* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
* examples/USER/yaff

27
doc/src/kspace_style.rst
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@ -11,26 +11,30 @@ Syntax
kspace_style style value
* style = *none* or *ewald* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
.. parsed-literal::
*none* value = none
*ewald* value = accuracy
accuracy = desired relative error in forces
*ewald/disp* value = accuracy
accuracy = desired relative error in forces
*ewald/omp* value = accuracy
accuracy = desired relative error in forces
*ewald/dipole* value = accuracy
accuracy = desired relative error in forces
*ewald/dipole/spin* value = accuracy
accuracy = desired relative error in forces
*ewald/disp* value = accuracy
accuracy = desired relative error in forces
*ewald/omp* value = accuracy
accuracy = desired relative error in forces
*pppm* value = accuracy
accuracy = desired relative error in forces
*pppm/cg* values = accuracy (smallq)
accuracy = desired relative error in forces
smallq = cutoff for charges to be considered (optional) (charge units)
*pppm/dipole* value = accuracy
accuracy = desired relative error in forces
*pppm/dipole/spin* value = accuracy
accuracy = desired relative error in forces
*pppm/disp* value = accuracy
accuracy = desired relative error in forces
*pppm/tip4p* value = accuracy
@ -41,22 +45,23 @@ Syntax
accuracy = desired relative error in forces
*pppm/intel* value = accuracy
accuracy = desired relative error in forces
*pppm/disp/intel* value = accuracy
accuracy = desired relative error in forces
*pppm/kk* value = accuracy
accuracy = desired relative error in forces
*pppm/omp* value = accuracy
accuracy = desired relative error in forces
*pppm/cg/omp* value = accuracy
*pppm/cg/omp* values = accuracy (smallq)
accuracy = desired relative error in forces
*pppm/disp/intel* value = accuracy
smallq = cutoff for charges to be considered (optional) (charge units)
*pppm/disp/omp* value = accuracy
accuracy = desired relative error in forces
*pppm/tip4p/omp* value = accuracy
accuracy = desired relative error in forces
*pppm/disp/tip4p/omp* value = accuracy
accuracy = desired relative error in forces
*pppm/stagger* value = accuracy
accuracy = desired relative error in forces
*pppm/dipole* value = accuracy
accuracy = desired relative error in forces
*pppm/dipole/spin* value = accuracy
accuracy = desired relative error in forces
*msm* value = accuracy
accuracy = desired relative error in forces
*msm/cg* value = accuracy (smallq)

6
doc/src/pair_lj.rst
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@ -90,6 +90,9 @@ pair\_style lj/cut/coul/wolf/omp command
pair\_style lj/cut/tip4p/cut command
====================================
pair\_style lj/cut/tip4p/cut/gpu command
========================================
pair\_style lj/cut/tip4p/cut/omp command
========================================
@ -102,9 +105,6 @@ pair\_style lj/cut/tip4p/long/omp command
pair\_style lj/cut/tip4p/long/opt command
=========================================
pair\_style lj/cut/tip4p/long/gpu command
=====================================
Syntax
""""""

0
doc/src/pair_lj_switch3_coulgauss.rst → doc/src/pair_lj_switch3_coulgauss_long.rst
View File

2
doc/src/pair_mm3_switch3_coulgauss.rst → doc/src/pair_mm3_switch3_coulgauss_long.rst
View File

@ -37,7 +37,7 @@ Examples
Description
"""""""""""
The *mm3/switch3/coulgauss* style evaluates the MM3
The *mm3/switch3/coulgauss/long* style evaluates the MM3
vdW potential :ref:`(Allinger) <mm3-allinger1989>`
.. image:: Eqs/pair_mm3_switch3.jpg

4
doc/src/pair_style.rst
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@ -231,7 +231,7 @@ accelerated styles exist.
* :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
* :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
* `lj/switch3/coulgauss <pair_lj_switch3_coulgauss>`_ - smoothed LJ vdW potential with Gaussian electrostatics
* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed LJ vdW potential with Gaussian electrostatics
* :doc:`lj96/cut <pair_lj96>` - Lennard-Jones 9/6 potential
* :doc:`local/density <pair_local_density>` - generalized basic local density potential
* :doc:`lubricate <pair_lubricate>` - hydrodynamic lubrication forces
@ -245,7 +245,7 @@ accelerated styles exist.
* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
* :doc:`mie/cut <pair_mie>` - Mie potential
* `mm3/switch3/coulgauss <pair_mm3_switch3_coulgauss>`_ - smoothed MM3 vdW potential with Gaussian electrostatics
* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
* :doc:`morse <pair_morse>` - Morse potential
* :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential