diff --git a/doc/src/Howto_amoeba.rst b/doc/src/Howto_amoeba.rst index b804fb8d1a..44458fcfdc 100644 --- a/doc/src/Howto_amoeba.rst +++ b/doc/src/Howto_amoeba.rst @@ -6,10 +6,10 @@ Ponder's group at the U Washington at St Louis. Their implementation in LAMMPS was done using F90 code provided by the Ponder group from their `Tinker MD code `_. -The current implementaion (May 2022) of AMOEBA in LAMMPS matches the +The current implementation (July 2022) of AMOEBA in LAMMPS matches the version discussed in :ref:`(Ponder) `, :ref:`(Ren) `, and :ref:`(Shi) `. Likewise the current -implementaion of HIPPO in LAMMPS matches the version discussed in +implementation of HIPPO in LAMMPS matches the version discussed in :ref:`(Rackers) `. These force fields can be used when polarization effects are desired @@ -140,7 +140,7 @@ amoeba/bitorsion ` command be defined. In the example above, the IDs for these two fixes are *pit* and *bit*. Of course, if the system being modeled does not have one or more of -the following -- bond, angle, dihedral, improper, pitorision, +the following -- bond, angle, dihedral, improper, pitorsion, bitorsion interactions -- then the corresponding style and fix commands above do not need to be used. See the example scripts in examples/amoeba for water systems as examples; they are simpler than @@ -157,7 +157,7 @@ namely a PRM and KEY file. The keyfile can be specified as NULL and default values for a various settings will be used. Note that these 2 files are meant to allow use of native Tinker files as-is. However LAMMPS does not support all the options which can be included -in a Tinker PRM or KEY file. See specifis below. +in a Tinker PRM or KEY file. See specifics below. A :doc:`special_bonds ` command with the *one/five* option is required, since the AMOEBA/HIPPO force fields define @@ -308,11 +308,11 @@ compatible with the LAMMPS data file format. .. _howto-Ponder: -**(Ponder)** Ponder, Wu, Ren, Pande, Chodera†, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549–2564 (2010). +**(Ponder)** Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010). .. _howto-Rackers: -**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056–7084 (2021). +**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021). .. _howto-Ren: @@ -320,5 +320,5 @@ compatible with the LAMMPS data file format. .. _howto-Shi: -**(Shi)** Shi, Xiz, Znahg, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013. +**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013. diff --git a/doc/src/angle_amoeba.rst b/doc/src/angle_amoeba.rst index 5ff286c8db..265c4812f9 100644 --- a/doc/src/angle_amoeba.rst +++ b/doc/src/angle_amoeba.rst @@ -41,8 +41,8 @@ length. These formulas match how the Tinker MD code performs its angle calculations for the AMOEBA and HIPPO force fields. See the -:doc:`Howto amoeba ` doc page for more information about -the implemention of AMOEBA and HIPPO in LAMMPS. +:doc:`Howto amoeba ` page for more information about +the implementation of AMOEBA and HIPPO in LAMMPS. Note that the :math:`E_a` and :math:`E_{ba}` formulas are identical to those used for the :doc:`angle_style class2/p6 ` @@ -75,7 +75,7 @@ restart files read by the :doc:`read_data ` or These are the 8 coefficients for the :math:`E_a` formula: * pflag = 0 or 1 -* ublag = 0 or 1 +* ubflag = 0 or 1 * :math:`\theta_0` (degrees) * :math:`K_2` (energy) * :math:`K_3` (energy) @@ -87,7 +87,7 @@ A pflag value of 0 vs 1 selects between the "in-plane" and "out-of-plane" options described above. Ubflag is 1 if there is a Urey-Bradley term associated with this angle type, else it is 0. :math:`\theta_0` is specified in degrees, but LAMMPS converts it to -radians internally; hence the various :math:`K` vaues are effectively +radians internally; hence the various :math:`K` values are effectively energy per radian\^2 or radian\^3 or radian\^4 or radian\^5 or radian\^6. diff --git a/doc/src/fix_amoeba_bitorsion.rst b/doc/src/fix_amoeba_bitorsion.rst index 2a4a4a62d9..74b3aced49 100644 --- a/doc/src/fix_amoeba_bitorsion.rst +++ b/doc/src/fix_amoeba_bitorsion.rst @@ -30,8 +30,8 @@ This command enables 5-body torsion/torsion interactions to be added to simulations which use the AMOEBA and HIPPO force fields. It matches how the Tinker MD code computes its torsion/torsion interactions for the AMOEBA and HIPPO force fields. See the -:doc:`Howto amoeba ` doc page for more information about -the implemention of AMOEBA and HIPPO in LAMMPS. +:doc:`Howto amoeba ` doc page for more information about +the implementation of AMOEBA and HIPPO in LAMMPS. Bitorsion interactions add additional potential energy contributions to pairs of overlapping phi-psi dihedrals of amino-acids, which are diff --git a/doc/src/fix_amoeba_pitorsion.rst b/doc/src/fix_amoeba_pitorsion.rst index 638f72c2d3..9653807143 100644 --- a/doc/src/fix_amoeba_pitorsion.rst +++ b/doc/src/fix_amoeba_pitorsion.rst @@ -30,7 +30,7 @@ This command enables 6-body pitorsion interactions to be added to simulations which use the AMOEBA and HIPPO force fields. It matches how the Tinker MD code computes its pitorsion interactions for the AMOEBA and HIPPO force fields. See the :doc:`Howto amoeba -` doc page for more information about the implemention +` doc page for more information about the implementation of AMOEBA and HIPPO in LAMMPS. Pitorsion interactions add additional potential energy contributions diff --git a/doc/src/improper_amoeba.rst b/doc/src/improper_amoeba.rst index b5507235a2..9b8260b853 100644 --- a/doc/src/improper_amoeba.rst +++ b/doc/src/improper_amoeba.rst @@ -35,8 +35,8 @@ This formula seems like a simplified version of the formula for the :math:`\chi_0` = 0.0. However the computation of the angle :math:`\chi` is done differently to match how the Tinker MD code computes its out-of-plane improper for the AMOEBA and HIPPO force -fields. See the :doc:`Howto amoeba ` doc page for more -information about the implemention of AMOEBA and HIPPO in LAMMPS. +fields. See the :doc:`Howto amoeba ` doc page for more +information about the implementation of AMOEBA and HIPPO in LAMMPS. If the 4 atoms in an improper quadruplet (listed in the data file read by the :doc:`read_data ` command are ordered I,J,K,L then diff --git a/doc/src/pair_amoeba.rst b/doc/src/pair_amoeba.rst index 726917624f..a58eb2fabc 100644 --- a/doc/src/pair_amoeba.rst +++ b/doc/src/pair_amoeba.rst @@ -32,7 +32,7 @@ Examples Additional info """"""""""""""" -* :doc:`Howto amoeba ` +* :doc:`Howto amoeba ` * examples/amoeba * tools/amoeba * potentials/\*.amoeba @@ -41,10 +41,10 @@ Additional info Description """"""""""" -The *amoeba* style computes the AMOEBA polarizeable field formulated +The *amoeba* style computes the AMOEBA polarizable field formulated by Jay Ponder's group at the U Washington at St Louis :ref:`(Ren) `, :ref:`(Shi) `. The *hippo* style computes -the HIPPO polarizeable force field, an extension to AMOEBA, formulated +the HIPPO polarizable force field, an extension to AMOEBA, formulated by Josh Rackers and collaborators in the Ponder group :ref:`(Rackers) `. @@ -56,7 +56,7 @@ the LAMMPS potentials directory with a "amoeba" or "hippo" suffix can be used. The Tinker distribution and website have additional force field files as well. -As discussed on the :doc:`Howto amoeba ` doc page, the +As discussed on the :doc:`Howto amoeba ` doc page, the intermolecular (non-bonded) portion of the AMOEBA force field contains these terms: @@ -76,7 +76,7 @@ Conceptually, these terms compute the following interactions: * :math:`U_{repulsion}` = Pauli repulsion due to rearrangement of electron density * :math:`U_{dispersion}` = dispersion between correlated, instantaneous induced dipole moments * :math:`U_{multipole}` = electrostatics between permanent point charges, dipoles, and quadrupoles -* :math:`U_{polar}` = electronic polarization bewteen induced point dipoles +* :math:`U_{polar}` = electronic polarization between induced point dipoles * :math:`U_{qxfer}` = charge transfer effects Note that the AMOEBA versus HIPPO force fields typically compute the @@ -121,10 +121,10 @@ The implementation of the AMOEBA and HIPPO force fields in LAMMPS was done using F90 code provided by the Ponder group from their `Tinker MD code `_. -The current implementaion (May 2022) of AMOEBA in LAMMPS matches the +The current implementation (July 2022) of AMOEBA in LAMMPS matches the version discussed in :ref:`(Ponder) `, :ref:`(Ren) -`, and :ref:`(Shi) `. Likewise th current -implementaion of HIPPO in LAMMPS matches the version discussed in +`, and :ref:`(Shi) `. Likewise the current +implementation of HIPPO in LAMMPS matches the version discussed in :ref:`(Rackers) `. ---------- @@ -146,12 +146,12 @@ lines. A Tinker KEY file is composed of lines, each of which has a keyword followed by zero or more parameters. The list of PRM sections and KEY keywords which LAMMPS recognizes are -listed on the :doc:`Howto amoeba ` doc page. If not +listed on the :doc:`Howto amoeba ` doc page. If not recognized, the section or keyword is skipped. Note that if the KEY file is specified as NULL, then no file is required; default values for various AMOEBA/HIPPO settings are used. -The :doc:`Howto amoeba ` doc page also gives the default +The :doc:`Howto amoeba ` doc page also gives the default settings. ---------- @@ -181,9 +181,9 @@ enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. The AMOEBA and HIPPO potential (PRM) and KEY files provided with -LAMMPS in the potentials and examples/amoeva directories are Tinker +LAMMPS in the potentials and examples/amoeba directories are Tinker files parameterized for Tinker units. Their numeric parameters are -converted by LAMMPS to its real units :doc:`units `. Thus uou +converted by LAMMPS to its real units :doc:`units `. Thus you can only use these pair styles with real units. These potentials do not yet calculate per-atom energy or virial @@ -237,11 +237,11 @@ none .. _amoeba-Ponder: -**(Ponder)** Ponder, Wu, Ren, Pande, Chodera†, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549–2564 (2010). +**(Ponder)** Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010). -.. _amobea-Rackers: +.. _amoeba-Rackers: -**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056–7084 (2021). +**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021). .. _amoeba-Ren: @@ -249,5 +249,5 @@ none .. _amoeba-Shi: -**(Shi)** Shi, Xiz, Znahg, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013. +**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 77a1da6643..d5cd578da0 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -269,6 +269,7 @@ binutils biomolecular biomolecule Biomolecules +biomolecules Biophys Biosym biquadratic @@ -278,6 +279,7 @@ Bispectrum bitbucket bitmapped bitmask +bitorsion bitrate bitrates Bitzek @@ -443,6 +445,7 @@ chiralIDs ChiralIDs chirality Cho +Chodera ChooseOffset chris Christoph @@ -577,6 +580,7 @@ cstring cstyle csvr ctrl +ctrn ctypes Ctypes cuda @@ -697,6 +701,7 @@ devel Devemy deviatoric Devine +dewald df dfftw DFT @@ -774,6 +779,7 @@ DPD dpdTheta dphi DPhil +dpme dr dR dragforce @@ -1277,6 +1283,7 @@ gzipped Haak Hafskjold halfstepback +halgren Halperin Halver Hamaker @@ -1284,6 +1291,7 @@ Hamel Hammerschmidt Hanley haptic +Haque Hara Harpertown Harting @@ -1627,6 +1635,7 @@ Kemper kepler keV Keyes +keyfile Khersonskii Khrapak Khvostov @@ -1702,6 +1711,7 @@ Ladd lagrangian lambdai LambdaLanczos +Lambrecht lamda lammps Lammps @@ -2087,6 +2097,7 @@ mlparks Mniszewski mnt mobi +Mobley modc Modell modelled @@ -2137,6 +2148,7 @@ mpiexec mpiio mpirun mplayer +mpole mps mradius Mrovec @@ -2171,6 +2183,7 @@ multicore multielectron multinode multiphysics +Multipole multiscale multisectioning multithreading @@ -2358,6 +2371,7 @@ nodesets Noehring Noffset noforce +noguess Noid nolib nonequilibrium @@ -2366,6 +2380,7 @@ nonGaussian nonlocal Nonlocal Noordhoek +noprecond nopreliminary Nord norder @@ -2542,6 +2557,7 @@ palegreen paleturquoise palevioletred Panagiotopoulos +Pande Pandit Papaconstantopoulos papayawhip @@ -2576,6 +2592,7 @@ Pavia Paxton pbc pc +pcg pchain Pchain pcmoves @@ -2609,7 +2626,9 @@ Persp peru Peskin Pettifor +pewald pfactor +pflag pgi ph Philipp @@ -2642,6 +2661,7 @@ pIp Pisarev Pishevar Pitera +pitorsion pj pjintve pKa @@ -2657,6 +2677,7 @@ plt plumedfile pmb pmcmoves +pme Pmolrotate Pmoltrans pN @@ -2681,6 +2702,7 @@ polyelectrolyte polyhedra Polym polymorphism +Ponder popen Popoola Popov @@ -2699,6 +2721,7 @@ potin Pourtois powderblue PowerShell +ppme ppn pppm Prakash @@ -2708,6 +2731,7 @@ pre Pre prec precession +precond prefactor prefactors prepend @@ -2802,6 +2826,8 @@ Qsb qtb quadratically quadrupolar +quadrupole +quadrupoles Quant quartic quat @@ -2818,6 +2844,7 @@ qw qx qy qz +Rackers radialscreened radialscreenedspin radialspin @@ -3057,6 +3084,7 @@ Schimansky Schiotz Schlitter Schmid +Schnieders Schoen Schotte Schratt @@ -3513,6 +3541,9 @@ Tz Tzou ub Uberuaga +ubflag +Ubflag +ubiquitin uca uChem uCond @@ -3566,12 +3597,14 @@ upenn upto Urbakh Urbana +UreyBradley Usabiaga usec uSemiParallel userguide username usleep +usolve usr util utils @@ -3605,6 +3638,7 @@ Vcm vdfmax vdim vdisplace +vdw vdW vdwl vec @@ -3758,6 +3792,7 @@ Xeon xflag xhi xHost +Xia Xiaohu Xiaowang Xie