diff --git a/doc/src/bond_mm3.rst b/doc/src/bond_mm3.rst index aa219f0cc7..585794da65 100644 --- a/doc/src/bond_mm3.rst +++ b/doc/src/bond_mm3.rst @@ -26,14 +26,14 @@ as defined in :ref:`(Allinger) ` .. math:: - E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right] + E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + \frac{7}{12} 2.55^2(r-r_0)^2 \right] where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a -prefactor. The anharmonic prefactors have units angstrom\^(-n): --2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes +prefactor. The anharmonic prefactors have units :math:`\AA^{-n}`: +:math:`-2.55 \AA^{-1}` and :math:`\frac{7}{12} 2.55^2 \AA^{-2}`. The code takes care of the necessary unit conversion for these factors internally. -Note that the MM3 papers contains an error in Eq (1): -(7/12)2.55 should be replaced with (7/12)2.55\^2 +Note that the MM3 papers contain an error in Eq (1): +:math:`\frac{7}{12} 2.55` should be replaced with :math:`\frac{7}{12} 2.55^2` The following coefficients must be defined for each bond type via the :doc:`bond_coeff ` command as in the example above, or in diff --git a/doc/src/compute_chunk_atom.rst b/doc/src/compute_chunk_atom.rst index d151692771..9bca1e26d1 100644 --- a/doc/src/compute_chunk_atom.rst +++ b/doc/src/compute_chunk_atom.rst @@ -602,8 +602,7 @@ be used. For non-orthogonal (triclinic) simulation boxes, only the *reduced* option may be used. A *box* value selects standard distance units as defined by the -:doc:`units ` command (e.g., :math:`\mathrm{\mathring A}` -for units = *real* or *metal*). +:doc:`units ` command (e.g., :math:`\AA` for units = *real* or *metal*). A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacing. A *reduced* value means normalized diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index fc063cea50..5d52ab947d 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -95,7 +95,7 @@ something like the following commands: refresh c_dsp delay 100 The :doc:`dump_modify thresh ` command will only output -atoms that have displaced more than :math:`0.6~\mathrm{\mathring A}` on each +atoms that have displaced more than :math:`0.6~\AA` on each snapshot (assuming metal units). The dump_modify *refresh* option triggers a call to this compute at the end of every dump. diff --git a/doc/src/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst index 78f784ff75..612fc28365 100644 --- a/doc/src/compute_entropy_atom.rst +++ b/doc/src/compute_entropy_atom.rst @@ -97,13 +97,13 @@ by the corresponding volume. This option can be useful when dealing with inhomogeneous systems such as those that have surfaces. Here are typical input parameters for fcc aluminum (lattice -constant :math:`4.05~\mathrm{\mathring A}`), +constant :math:`4.05~\AA`), .. parsed-literal:: compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 -and for bcc sodium (lattice constant 4.23 Angstroms), +and for bcc sodium (lattice constant :math:`4.23~\AA`), .. parsed-literal:: diff --git a/doc/src/compute_rigid_local.rst b/doc/src/compute_rigid_local.rst index 456fc57c38..91e0dc0acf 100644 --- a/doc/src/compute_rigid_local.rst +++ b/doc/src/compute_rigid_local.rst @@ -109,8 +109,7 @@ The *mass* attribute is the total mass of the rigid body. There are two options for outputting the coordinates of the center of mass (COM) of the body. The *x*, *y*, *z* attributes write the COM "unscaled", in the appropriate distance :doc:`units ` -(:math:`\mathrm{\mathring A}`, -sigma, etc). Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by +(:math:`\AA`, :math:`\sigma`, etc). Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by the image flags for each body. Unwrapped means that if the body COM has passed through a periodic boundary one or more times, the value is generated what the COM coordinate would be if it had not been diff --git a/doc/src/compute_saed.rst b/doc/src/compute_saed.rst index 1a746ab7b9..c2e1f3d1e0 100644 --- a/doc/src/compute_saed.rst +++ b/doc/src/compute_saed.rst @@ -86,7 +86,7 @@ will defined using the *c* values for the spacing along each reciprocal lattice axis. Note that manual mapping of the reciprocal space mesh is good for comparing diffraction results from multiple simulations; however it can reduce the likelihood that Bragg reflections will be satisfied -unless small spacing parameters (:math:`<0.05~\mathrm{\mathring A}^-1`) +unless small spacing parameters (:math:`<0.05~\AA^-1`) are implemented. Meshes with manual spacing do not require a periodic boundary. diff --git a/doc/src/compute_temp_ramp.rst b/doc/src/compute_temp_ramp.rst index 5c18243c23..2e170316fb 100644 --- a/doc/src/compute_temp_ramp.rst +++ b/doc/src/compute_temp_ramp.rst @@ -58,7 +58,7 @@ constant, and :math:`T` is the absolute temperature. The *units* keyword determines the meaning of the distance units used for coordinates (*clo*, *chi*) and velocities (*vlo*, *vhi*). A *box* value selects standard distance units as defined by the :doc:`units ` -command (e.g., :math:`\mathrm{\mathring{A}}` for units = real or metal). A +command (e.g., :math:`\AA` for units = real or metal). A *lattice* value means the distance units are in lattice spacings (i.e., velocity in lattice spacings per unit time). The :doc:`lattice ` command must have been previously used to define the lattice spacing. diff --git a/doc/src/compute_xrd.rst b/doc/src/compute_xrd.rst index 10ee35496d..8673ce9199 100644 --- a/doc/src/compute_xrd.rst +++ b/doc/src/compute_xrd.rst @@ -91,7 +91,7 @@ reciprocal lattice axis. Note that manual mapping of the reciprocal space mesh is good for comparing diffraction results from multiple simulations; however, it can reduce the likelihood that Bragg reflections will be satisfied unless small spacing parameters -(:math:`< 0.05~\mathrm{\mathring{A}}^{-1}`) are implemented. +(:math:`< 0.05~\AA^{-1}`) are implemented. Meshes with manual spacing do not require a periodic boundary. The limits of the reciprocal lattice mesh are determined by range of diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index 17df11a5bf..95d0abd240 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -464,7 +464,7 @@ The *units* keyword determines the meaning of the distance units used to specify the coordinates of the one particle created by the *single* style, or the overlap distance *Doverlap* by the *overlap* keyword. A *box* value selects standard distance units as defined by the -:doc:`units ` command (e.g., :math:`\mathrm{\mathring{A}}` for +:doc:`units ` command (e.g., :math:`\AA` for units = *real* or *metal*\ . A *lattice* value means the distance units are in lattice spacings. diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index d9bf367ec4..0055fd584f 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -104,7 +104,7 @@ atom's rotation. Distance units for displacements and the origin point of the *rotate* style are determined by the setting of *box* or *lattice* for the *units* keyword. *Box* means distance units as defined by the -:doc:`units ` command (e.g., :math:`\mathrm{\mathring A}` for +:doc:`units ` command (e.g., :math:`\AA` for *real* or *metal* units). *Lattice* means distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to define the lattice spacing. diff --git a/doc/src/dump.rst b/doc/src/dump.rst index f069911096..7ac6a7ed54 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -693,7 +693,7 @@ charge. There are several options for outputting atom coordinates. The *x*, *y*, and *z* attributes write atom coordinates "unscaled", in the -appropriate distance :doc:`units ` (:math:`\mathrm{\mathring A}`, +appropriate distance :doc:`units ` (:math:`\AA`, :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 diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 0d059581eb..52a36e1b00 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -632,7 +632,7 @@ calculates the displacement of each atom from its reference position. The "4" index is the scalar displacement; 1, 2, and 3 are the :math:`xyz` components of the displacement. The :doc:`dump_modify thresh ` command will cause only atoms that have displaced more than -:math:`0.6~\mathrm{\mathring A}` to be output on a given snapshot (assuming +:math:`0.6~\AA` to be output on a given snapshot (assuming metal units). However, note that when an atom is output, we also need to update the reference position for that atom to its new coordinates. So that it will not be output in every snapshot thereafter. That reference position is @@ -675,7 +675,7 @@ value of *yes* means atom coords are written in normalized units from 0.0 to 1.0 in each box dimension. If the simulation box is triclinic (tilted), then all atom coords will still be between 0.0 and 1.0. A value of *no* means they are written in absolute distance units -(e.g., :math:`\mathrm{\mathring A}` or :math:`\sigma`). +(e.g., :math:`\AA` or :math:`\sigma`). Using this keyword will reset all custom header names set with *dump_modify colname* to their respective default values. @@ -687,7 +687,7 @@ when writing to XTC files. By default, they are initialized for whatever :doc:`units ` style is being used, to write out coordinates in nanometers and time in picoseconds. For example, for *real* units, LAMMPS defines *sfactor* = 0.1 and *tfactor* = 0.001, since the -:math:`\mathrm{\mathring A}` and fs used by *real* units are 0.1 nm and +:math:`\AA` and fs used by *real* units are 0.1 nm and 0.001 ps, respectively. If you are using a units system with distance and time units far from nm and ps, you may wish to write XTC files with different units, since the compression algorithm used in XTC files is diff --git a/doc/src/fix_acks2_reaxff.rst b/doc/src/fix_acks2_reaxff.rst index 9f7cc5303d..ebb1b48051 100644 --- a/doc/src/fix_acks2_reaxff.rst +++ b/doc/src/fix_acks2_reaxff.rst @@ -71,7 +71,7 @@ potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the bond cutoff distance. Note that these 4 quantities are also in the ReaxFF potential file, except that eta is defined here as twice the eta value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units -of this fix are hard-coded to be :math:`\mathrm{\mathring{A}}`, eV, and +of this fix are hard-coded to be :math:`\AA`, eV, and electronic charge. The optional *maxiter* keyword allows changing the max number @@ -111,7 +111,7 @@ LAMMPS was built with that package. See the :doc:`Build package This fix does not correctly handle interactions involving multiple periodic images of the same atom. Hence, it should not be used for -periodic cell dimensions less than :math:`10~\mathrm{\mathring{A}}`. +periodic cell dimensions less than :math:`10~\AA`. This fix may be used in combination with :doc:`fix efield ` and will apply the external electric field during charge equilibration, diff --git a/doc/src/fix_append_atoms.rst b/doc/src/fix_append_atoms.rst index 7c52d9b431..c31d4ff9da 100644 --- a/doc/src/fix_append_atoms.rst +++ b/doc/src/fix_append_atoms.rst @@ -79,7 +79,7 @@ measured from zhi and is set with the *extent* argument. The *units* keyword determines the meaning of the distance units used to define a wall position, but only when a numeric constant is used. A *box* value selects standard distance units as defined by the -:doc:`units ` command (e.g., :math:`\mathrm{\mathring A}` +:doc:`units ` command (e.g., :math:`\AA` for units = real or metal. A *lattice* value means the distance units are in lattice spacings. The :doc:`lattice ` command must have been previously used to diff --git a/doc/src/fix_bocs.rst b/doc/src/fix_bocs.rst index 566bf8e68d..018418c538 100644 --- a/doc/src/fix_bocs.rst +++ b/doc/src/fix_bocs.rst @@ -59,7 +59,7 @@ Note both the COMMA and the SPACE separating the volume's value and its corresponding pressure correction. The volumes in the file must be uniformly spaced. Both the volumes and the pressure corrections should be provided in the proper units, e.g. if you are using *units real*, -the volumes should all be in cubic angstroms, and the pressure corrections +the volumes should all be in cubic Angstroms, and the pressure corrections should all be in atmospheres. Furthermore, the table should start/end at a volume considerably smaller/larger than you expect your system to sample during the simulation. If the system ever reaches a volume outside of the @@ -72,8 +72,8 @@ With the *analytic* option, the arguments are as follows: ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N Note that *V_avg* and *Coeff_i* should all be in the proper units, e.g. if you -are using *units real*, *V_avg* should be in cubic angstroms, and the -coefficients should all be in atmospheres \* cubic angstroms. +are using *units real*, *V_avg* should be in cubic Angstroms, and the +coefficients should all be in atmospheres \* cubic Angstroms. ---------- diff --git a/doc/src/fix_imd.rst b/doc/src/fix_imd.rst index 06d8787b1b..e29da08c4c 100644 --- a/doc/src/fix_imd.rst +++ b/doc/src/fix_imd.rst @@ -88,8 +88,8 @@ to send "unwrapped" coordinates to the IMD client that undo the wrapping back of coordinates into the principle unit cell, as done by default in LAMMPS. The *fscale* keyword allows to apply a scaling factor to forces transmitted by the IMD client. The IMD protocols -stipulates that forces are transferred in kcal/mol/angstrom under the -assumption that coordinates are given in angstrom. For LAMMPS runs +stipulates that forces are transferred in kcal/mol/Angstrom under the +assumption that coordinates are given in Angstrom. For LAMMPS runs with different units or as a measure to tweak the forces generated by the manipulation of the IMD client, this option allows to make adjustments. diff --git a/doc/src/fix_qeq_reaxff.rst b/doc/src/fix_qeq_reaxff.rst index 906847f90a..db9015f187 100644 --- a/doc/src/fix_qeq_reaxff.rst +++ b/doc/src/fix_qeq_reaxff.rst @@ -124,7 +124,7 @@ LAMMPS was built with that package. See the :doc:`Build package This fix does not correctly handle interactions involving multiple periodic images of the same atom. Hence, it should not be used for -periodic cell dimensions less than 10 angstroms. +periodic cell dimensions less than 10 Angstroms. This fix may be used in combination with :doc:`fix efield ` and will apply the external electric field during charge equilibration, diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 0852a728a4..cbaa82d547 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -301,7 +301,7 @@ and for mixed periodic and non-periodic boundaries. MSM is most competitive versus Ewald and PPPM when only relatively low accuracy forces, about 1e-4 relative error or less accurate, are needed. Note that use of a larger Coulombic cutoff (i.e. 15 -angstroms instead of 10 angstroms) provides better MSM accuracy for +Angstroms instead of 10 Angstroms) provides better MSM accuracy for both the real space and grid computed forces. Currently calculation of the full pressure tensor in MSM is expensive. diff --git a/doc/src/pair_airebo.rst b/doc/src/pair_airebo.rst index b250064476..9a1e4e5518 100644 --- a/doc/src/pair_airebo.rst +++ b/doc/src/pair_airebo.rst @@ -102,7 +102,7 @@ a few fitted spline values are slightly different. For most cases the statistical averages as the original REBO potential from which it was derived. The :math:`E^{\text{REBO}}` term in the AIREBO potential gives the model its reactive capabilities and only describes short-ranged C-C, C-H and H-H -interactions (:math:`r < 2` Angstroms). These interactions have strong +interactions (:math:`r < 2 \AA`). These interactions have strong coordination-dependence through a bond order parameter, which adjusts the attraction between the I,J atoms based on the position of other nearby atoms and thus has 3- and 4-body dependence. @@ -116,9 +116,9 @@ interactions is determined by the *cutoff* argument to the pair_style command which is a scale factor. For each type pair (C-C, C-H, H-H) the cutoff is obtained by multiplying the scale factor by the sigma value defined in the potential file for that type pair. In the -standard AIREBO potential, :math:`\sigma_{CC} = 3.4` Angstroms, so with a scale +standard AIREBO potential, :math:`\sigma_{CC} = 3.4 \AA`, so with a scale factor of 3.0 (the argument in pair_style), the resulting :math:`E^{\text{LJ}}` cutoff -would be 10.2 Angstroms. +would be :math:`10.2 \AA`. By default, the longer-ranged interaction is smoothly switched off between 2.16 and 3.0 :math:`\sigma`. By specifying *cutoff_min* in addition diff --git a/doc/src/pair_smtbq.rst b/doc/src/pair_smtbq.rst index 50b4afaf2d..ea55b2f2d9 100644 --- a/doc/src/pair_smtbq.rst +++ b/doc/src/pair_smtbq.rst @@ -182,19 +182,19 @@ For each cations (metal): * Potential parameter: - If type of potential is 'second_moment' : A (eV), *p*, - :math:`\zeta^0` (eV) and *q*, :math:`r_{c1} (\mathrm{\mathring{A}})`, :math:`r_{c2} - (\mathrm{\mathring{A}})` and :math:`r_0 (\mathrm{\mathring{A}})` - - If type of potential is 'buck' : *C* (eV) and :math:`\rho (\mathrm{\mathring{A}})` + :math:`\zeta^0` (eV) and *q*, :math:`r_{c1} (\AA)`, :math:`r_{c2} + (\AA)` and :math:`r_0 (\AA)` + - If type of potential is 'buck' : *C* (eV) and :math:`\rho (\AA)` - If type of potential is 'buckPlusAttr' : *C* (eV) and :math:`\rho - (\mathrm{\mathring{A}})` *D* (eV), *B* :math:`(\mathrm{\mathring{A}}^{-1})`, :math:`r^{OO}_1 (\mathrm{\mathring{A}})` and - :math:`r^{OO}_2 (\mathrm{\mathring{A}})` + (\AA)` *D* (eV), *B* :math:`(\AA^{-1})`, :math:`r^{OO}_1 (\AA)` and + :math:`r^{OO}_2 (\AA)` * Divider line 4) Tables parameters: * Cutoff radius for the Coulomb interaction (:math:`R_{coul}`) -* Starting radius (:math:`r_{min} = 1,18845 \mathrm{\mathring{A}}`) and increments - (:math:`dr = 0.001 \mathrm{\mathring{A}}`) for creating the potential table. +* Starting radius (:math:`r_{min} = 1,18845 \AA`) and increments + (:math:`dr = 0.001 \AA`) for creating the potential table. * Divider line 5) Rick model parameter: @@ -208,7 +208,7 @@ For each cations (metal): 6) Coordination parameter: * First (:math:`r_{1n}`) and second (:math:`r_{2n}`) neighbor distances - in angstrom + in Angstrom * Divider line 7) Charge initialization mode: diff --git a/doc/src/pair_zbl.rst b/doc/src/pair_zbl.rst index 6c698b23d2..1986fffa4d 100644 --- a/doc/src/pair_zbl.rst +++ b/doc/src/pair_zbl.rst @@ -73,7 +73,7 @@ be included in a pair_coeff command. The numerical values of the exponential decay constants in the screening function depend on the unit of distance. In the above - equation they are given for units of angstroms. LAMMPS will + equation they are given for units of Angstroms. LAMMPS will automatically convert these values to the distance unit of the specified LAMMPS :doc:`units ` setting. The values of Z should always be given as multiples of a proton's charge, e.g. 29.0 for diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index e8ba264495..aaa6b6bad5 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -221,7 +221,7 @@ impropers, and dihedrals can be computed on this innermost 0.5 fs step. The outermost timestep cannot be greater than 4.0 fs without risking energy drift. Smooth switching of forces between the levels of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2 -angstrom "healing distance" (the distance between the outer and inner +Angstrom "healing distance" (the distance between the outer and inner cutoffs) works reasonably well. We thus recommend the following settings for use of the *respa* style without SHAKE in biomolecular simulations: @@ -277,7 +277,7 @@ Even a LJ system can benefit from rRESPA if the interactions are divided by the inner, middle and outer keywords. A 2-fold or more speedup can be obtained while maintaining good energy conservation. In real units, for a pure LJ fluid at liquid density, with a sigma of -3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings +3.0 Angstroms, and epsilon of 0.1 Kcal/mol, the following settings seem to work well: .. code-block:: LAMMPS diff --git a/doc/utils/sphinx-config/conf.py.in b/doc/utils/sphinx-config/conf.py.in index c89aa8b4ae..c94fcaf1d2 100644 --- a/doc/utils/sphinx-config/conf.py.in +++ b/doc/utils/sphinx-config/conf.py.in @@ -159,7 +159,6 @@ pygments_style = 'default' # If true, keep warnings as "system message" paragraphs in the built documents. #keep_warnings = False - # -- Options for HTML output ---------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for @@ -264,8 +263,18 @@ else: html_math_renderer = 'mathjax' # use relative path for mathjax, so it is looked for in the -# html tree and the manual becomes readable when offline +# html tree and the manual becomes readable when offline mathjax_path = 'mathjax/es5/tex-mml-chtml.js' + +# hack to enable use of \AA in :math: +rst_prolog = r""" + +.. only:: html + + :math:`\renewcommand{\AA}{\text{Å}}` + +""" + # -- Options for LaTeX output --------------------------------------------- latex_elements = { @@ -278,6 +287,7 @@ latex_elements = { # Additional stuff for the LaTeX preamble. 'preamble': r''' \setcounter{tocdepth}{2} +\renewcommand{\AA}{\mbox{\textrm{\r{A}}}} ''' }