diff --git a/doc/src/compute.rst b/doc/src/compute.rst index e910598c7a..01f91835ec 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -213,7 +213,7 @@ The individual style names on the :doc:`Commands compute ` pag * :doc:`fep/ta ` - compute free energies for a test area perturbation * :doc:`force/tally ` - force between two groups of atoms via the tally callback mechanism * :doc:`fragment/atom ` - fragment ID for each atom -* :doc:`global/atom ` - +* :doc:`global/atom ` - assign global values to each atom from arrays of global values * :doc:`group/group ` - energy/force between two groups of atoms * :doc:`gyration ` - radius of gyration of group of atoms * :doc:`gyration/chunk ` - radius of gyration for each chunk diff --git a/doc/src/compute_cluster_atom.rst b/doc/src/compute_cluster_atom.rst index 2c20ffdd28..876186b6b6 100644 --- a/doc/src/compute_cluster_atom.rst +++ b/doc/src/compute_cluster_atom.rst @@ -69,9 +69,9 @@ fragments or not, based on the *yes* or *no* setting. If the setting is *no* (the default), their fragment IDs are set to 0. An aggregate is defined by combining the rules for clusters and -fragments, i.e. a set of atoms, where each of it is within the cutoff +fragments (i.e., a set of atoms, where each of them is within the cutoff distance from one or more atoms within a fragment that is part of -the same cluster. This measure can be used to track molecular assemblies +the same cluster). This measure can be used to track molecular assemblies like micelles. For computes *cluster/atom* and *aggregate/atom* a neighbor list @@ -92,9 +92,9 @@ style computes. does not apply when using long-range coulomb (\ *coul/long*, *coul/msm*, *coul/wolf* or similar. One way to get around this would be to set special_bond scaling factors to very tiny numbers that are not exactly - zero (e.g. 1.0e-50). Another workaround is to write a dump file, and - use the :doc:`rerun ` command to compute the clusters for - snapshots in the dump file. The rerun script can use a + zero (e.g., :math:`1.0 \times 10^{-50}`). Another workaround is to write a + dump file and use the :doc:`rerun ` command to compute the clusters + for snapshots in the dump file. The rerun script can use a :doc:`special_bonds ` command that includes all pairs in the neighbor list. @@ -114,7 +114,7 @@ any command that uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The per-atom vector values will be an ID > 0, as explained above. +The per-atom vector values will be an ID :math:`> 0`, as explained above. Restrictions """""""""""" @@ -129,5 +129,5 @@ Related commands Default """"""" -The default for fragment/atom is single no. +The default for fragment/atom is single=no. diff --git a/doc/src/compute_com.rst b/doc/src/compute_com.rst index cb5782efec..df5373293e 100644 --- a/doc/src/compute_com.rst +++ b/doc/src/compute_com.rst @@ -38,7 +38,8 @@ are the :math:`(x,y,z)` coordinates of the center of mass. "unwrapped" coordinates. See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags - (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + (e.g., to 0) before invoking this compute by using the + :doc:`set image ` command. Output info """"""""""" diff --git a/doc/src/compute_com_chunk.rst b/doc/src/compute_com_chunk.rst index 3165acfbcc..a2df80d5d8 100644 --- a/doc/src/compute_com_chunk.rst +++ b/doc/src/compute_com_chunk.rst @@ -6,7 +6,7 @@ compute com/chunk command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID com/chunk chunkID @@ -34,7 +34,7 @@ molecule or atoms in a spatial bin. See the :doc:`compute chunk/atom ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags - (e.g. to 0) before invoking this compute by using the :doc:`set image ` command. + (e.g., to 0) before invoking this compute by using the + :doc:`set image ` command. The simplest way to output the results of the compute com/chunk calculation to a file is to use the :doc:`fix ave/time ` @@ -70,13 +71,13 @@ Output info """"""""""" This compute calculates a global array where the number of rows = the -number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns = -3 for the x,y,z center-of-mass coordinates of each chunk. These +number of chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom ` command. The number of columns is +3 for the :math:`(x,y,z)` center-of-mass coordinates of each chunk. These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. -The array values are "intensive". The array values will be in +The array values are "intensive." The array values will be in distance :doc:`units `. Restrictions diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst index 23b5f4639d..31aa24aa60 100644 --- a/doc/src/compute_contact_atom.rst +++ b/doc/src/compute_contact_atom.rst @@ -6,7 +6,7 @@ compute contact/atom command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID contact/atom group2-ID @@ -44,11 +44,11 @@ accessed by any command that uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The per-atom vector values will be a number >= 0.0, as explained +The per-atom vector values will be a number :math:`\ge 0.0`, as explained above. The optional *group2-ID* argument allows to specify from which group atoms -contribute to the coordination number. Default setting is group 'all'. +contribute to the coordination number. Default setting is group 'all.' Restrictions """""""""""" diff --git a/doc/src/compute_coord_atom.rst b/doc/src/compute_coord_atom.rst index bff2a8a8af..54bdfbb2f6 100644 --- a/doc/src/compute_coord_atom.rst +++ b/doc/src/compute_coord_atom.rst @@ -9,7 +9,7 @@ Accelerator Variants: *coord/atom/kk* Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID coord/atom cstyle args ... @@ -19,13 +19,13 @@ Syntax .. parsed-literal:: - *cutoff* args = cutoff [group group2-ID] typeN - cutoff = distance within which to count coordination neighbors (distance units) - group *group2-ID* = select group-ID to restrict which atoms to consider for coordination number (optional) - typeN = atom type for Nth coordination count (see asterisk form below) - *orientorder* args = orientorderID threshold - orientorderID = ID of an orientorder/atom compute - threshold = minimum value of the product of two "connected" atoms + *cutoff* args = cutoff [group group2-ID] typeN + cutoff = distance within which to count coordination neighbors (distance units) + group *group2-ID* = select group-ID to restrict which atoms to consider for coordination number (optional) + typeN = atom type for Nth coordination count (see asterisk form below) + *orientorder* args = orientorderID threshold + orientorderID = ID of an orientorder/atom compute + threshold = minimum value of the product of two "connected" atoms Examples """""""" @@ -54,7 +54,7 @@ neighboring atoms, unless selected by type, type range, or group option, are included in the coordination number tally. The optional *group* keyword allows to specify from which group atoms -contribute to the coordination number. Default setting is group 'all'. +contribute to the coordination number. Default setting is group 'all.' The *typeN* keywords allow specification of which atom types contribute to each coordination number. One coordination number is @@ -65,15 +65,15 @@ includes atoms of all types (same as the "\*" format, see below). The *typeN* keywords can be specified in one of two ways. An explicit numeric value can be used, as in the second example above. Or a wild-card asterisk can be used to specify a range of atom types. This -takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of +takes the form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is the number of atom types, then an asterisk with no numeric values means all types -from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N +from 1 to :math:`N`. A leading asterisk means all types from 1 to n +(inclusive). A trailing asterisk means all types from m to :math:`N` (inclusive). A middle asterisk means all types from m to n (inclusive). The *orientorder* cstyle calculates the number of "connected" neighbor -atoms J around each central atom I. For this *cstyle*, connected is +atoms *j* around each central atom *i*\ . For this *cstyle*, connected is defined by the orientational order parameter calculated by the :doc:`compute orientorder/atom ` command. This *cstyle* thus allows one to apply the ten Wolde's criterion to @@ -84,16 +84,16 @@ The ID of the previously specified :doc:`compute orientorder/atom ` doc page for an overview of LAMMPS output options. -The per-atom vector or array values will be a number >= 0.0, as +The per-atom vector or array values will be a number :math:`\ge 0.0`, as explained above. Restrictions diff --git a/doc/src/compute_damage_atom.rst b/doc/src/compute_damage_atom.rst index 3847a4de66..b75a3ebc57 100644 --- a/doc/src/compute_damage_atom.rst +++ b/doc/src/compute_damage_atom.rst @@ -6,7 +6,7 @@ compute damage/atom command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID damage/atom @@ -48,7 +48,7 @@ any command that uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The per-atom vector values are unitless numbers (damage) >= 0.0. +The per-atom vector values are unitless numbers (damage) :math:`\ge 0.0`. Restrictions """""""""""" diff --git a/doc/src/compute_dihedral.rst b/doc/src/compute_dihedral.rst index d4198dde3c..1d987ec12f 100644 --- a/doc/src/compute_dihedral.rst +++ b/doc/src/compute_dihedral.rst @@ -6,7 +6,7 @@ compute dihedral command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID dihedral @@ -34,10 +34,12 @@ total energy contributed by one or more of the hybrid sub-styles. Output info """"""""""" -This compute calculates a global vector of length N where N is the -number of sub_styles defined by the :doc:`dihedral_style hybrid ` command. which can be accessed by indices -1-N. These values can be used by any command that uses global scalar -or vector values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output +This compute calculates a global vector of length :math:`N`, where :math:`N` +is the number of sub_styles defined by the +:doc:`dihedral_style hybrid ` command, which can be accessed by +the indices 1 through :math:`N`. These values can be used by any command that +uses global scalar or vector values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS output options. The vector values are "extensive" and will be in energy diff --git a/doc/src/compute_dihedral_local.rst b/doc/src/compute_dihedral_local.rst index 82d3c3ab72..291b870373 100644 --- a/doc/src/compute_dihedral_local.rst +++ b/doc/src/compute_dihedral_local.rst @@ -6,7 +6,7 @@ compute dihedral/local command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID dihedral/local value1 value2 ... keyword args ... @@ -35,7 +35,6 @@ Examples .. code-block:: LAMMPS compute 1 all dihedral/local phi - compute 1 all dihedral/local phi v_cos set phi p Description @@ -46,25 +45,26 @@ interactions. The number of datums generated, aggregated across all processors, equals the number of dihedral angles in the system, modified by the group parameter as explained below. -The value *phi* is the dihedral angle, as defined in the diagram on -the :doc:`dihedral_style ` doc page. +The value *phi* (:math:`\phi`) is the dihedral angle, as defined in the diagram +on the :doc:`dihedral_style ` doc page. -The value *v_name* can be used together with the *set* keyword to -compute a user-specified function of the dihedral angle phi. The -*name* specified for the *v_name* value is the name of an :doc:`equal-style variable ` which should evaluate a formula based on a -variable which will store the angle phi. This other variable must +The value *v_name* can be used together with the *set* keyword to compute a +user-specified function of the dihedral angle :math:`\phi`. The *name* +specified for the *v_name* value is the name of an +:doc:`equal-style variable ` which should evaluate a formula based on +a variable which will store the angle :math:`\phi`. This other variable must be an :doc:`internal-style variable ` defined in the input script; its initial numeric value can be anything. It must be an internal-style variable, because this command resets its value directly. The *set* keyword is used to identify the name of this -other variable associated with phi. +other variable associated with :math:`\phi`. -Note that the value of phi for each angle which stored in the internal +Note that the value of :math:`\phi` for each angle which stored in the internal variable is in radians, not degrees. As an example, these commands can be added to the bench/in.rhodo -script to compute the cosine and cosine\^2 of every dihedral angle in -the system and output the statistics in various ways: +script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every dihedral +angle in the system and output the statistics in various ways: .. code-block:: LAMMPS @@ -81,19 +81,18 @@ the system and output the statistics in various ways: fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo -The :doc:`dump local ` command will output the angle, -cosine(angle), cosine\^2(angle) for every dihedral in the system. The -:doc:`thermo_style ` command will print the average of +The :doc:`dump local ` command will output the angle (:math:`\phi`), +:math:`\cos(\phi)`, and :math:`\cos^2(\phi)` for every dihedral in the system. +The :doc:`thermo_style ` command will print the average of those quantities via the :doc:`compute reduce ` command with thermo output. And the :doc:`fix ave/histo ` -command will histogram the cosine(angle) values and write them to a -file. +command will histogram the cosine(angle) values and write them to a file. ---------- The local data stored by this command is generated by looping over all the atoms owned on a processor and their dihedrals. A dihedral will -only be included if all 4 atoms in the dihedral are in the specified +only be included if all four atoms in the dihedral are in the specified compute group. Note that as atoms migrate from processor to processor, there will be @@ -101,7 +100,8 @@ no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. -For example, dihedral output from the :doc:`compute property/local ` command can be combined +For example, dihedral output from the +:doc:`compute property/local ` command can be combined with data from this command and output by the :doc:`dump local ` command in a consistent way. @@ -120,9 +120,10 @@ This compute calculates a local vector or local array depending on the number of values. The length of the vector or number of rows in the array is the number of dihedrals. If a single value is specified, a local vector is produced. If two or more values are specified, a -local array is produced where the number of columns = the number of +local array is produced where the number of columns is equal to the number of values. The vector or array can be accessed by any command that uses -local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output +local values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS output options. The output for *phi* will be in degrees. diff --git a/doc/src/compute_dilatation_atom.rst b/doc/src/compute_dilatation_atom.rst index 0e3159ffe7..8e3c86a4af 100644 --- a/doc/src/compute_dilatation_atom.rst +++ b/doc/src/compute_dilatation_atom.rst @@ -6,12 +6,12 @@ compute dilatation/atom command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID dilatation/atom * ID, group-ID are documented in compute command -* dilation/atom = style name of this compute command +* dilatation/atom = style name of this compute command Examples """""""" @@ -30,13 +30,13 @@ for an overview of LAMMPS commands for Peridynamics modeling. For small deformation, dilatation of is the measure of the volumetric strain. -The dilatation "theta" for each peridynamic particle I is calculated -as a sum over its neighbors with unbroken bonds, where the -contribution of the IJ pair is a function of the change in bond length +The dilatation :math:`\theta` for each peridynamic particle :math:`i` is +calculated as a sum over its neighbors with unbroken bonds, where the +contribution of the :math:`ij` pair is a function of the change in bond length (versus the initial length in the reference state), the volume fraction of the particles and an influence function. See the -`PDLAMMPS user guide `_ for a formal -definition of dilatation. +`PDLAMMPS user guide `_ for +a formal definition of dilatation. This command can only be used with a subset of the Peridynamic :doc:`pair styles `: peri/lps, peri/ves and peri/eps. @@ -51,13 +51,14 @@ any command that uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The per-atom vector values are unitless numbers (theta) >= 0.0. +The per-atom vector values are unitless numbers :math:`(\theta \ge 0.0)`. Restrictions """""""""""" This compute is part of the PERI package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_dipole.rst b/doc/src/compute_dipole.rst index 243efc0576..ee45dede9f 100644 --- a/doc/src/compute_dipole.rst +++ b/doc/src/compute_dipole.rst @@ -6,7 +6,7 @@ compute dipole command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID dipole charge-correction @@ -43,7 +43,7 @@ and per-atom dipole moments, if present, contribute to the computed dipole. :doc:`dump custom ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are - set for each atom. You can reset the image flags (e.g. to 0) before + set for each atom. You can reset the image flags (e.g., to 0) before invoking this compute by using the :doc:`set image ` command. Output info @@ -54,8 +54,9 @@ the computed dipole moment and a global vector of length 3 with the dipole vector. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The computed values are "intensive". The array values will be in -dipole units, i.e. charge units times distance :doc:`units `. +The computed values are "intensive." The array values will be in +dipole units (i.e., charge :doc:`units ` times distance +:doc:`units `). Restrictions """""""""""" diff --git a/doc/src/compute_dipole_chunk.rst b/doc/src/compute_dipole_chunk.rst index fc1e8d7709..16d45b5608 100644 --- a/doc/src/compute_dipole_chunk.rst +++ b/doc/src/compute_dipole_chunk.rst @@ -6,7 +6,7 @@ compute dipole/chunk command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID dipole/chunk chunkID charge-correction @@ -38,8 +38,8 @@ or atoms in a spatial bin. See the :doc:`compute chunk/atom details of how chunks can be defined and examples of how they can be used to measure properties of a system. -This compute calculates the x,y,z coordinates of the dipole vector and -the total dipole moment for each chunk, which includes all effects due +This compute calculates the :math:`(x,y,z)` coordinates of the dipole vector +and the total dipole moment for each chunk, which includes all effects due to atoms passing through periodic boundaries. For chunks with a net charge the resulting dipole is made position independent by subtracting the position vector of the center of mass or geometric center times the @@ -62,7 +62,7 @@ chunk IDs. "unwrapped" coordinates. See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You can reset the image flags - (e.g. to 0) before invoking this compute by using the :doc:`set image + (e.g., to 0) before invoking this compute by using the :doc:`set image ` command. The simplest way to output the results of the compute com/chunk @@ -80,14 +80,15 @@ Output info This compute calculates a global array where the number of rows = the number of chunks *Nchunk* as calculated by the specified :doc:`compute -chunk/atom ` command. The number of columns = 4 for -the x,y,z dipole vector components and the total dipole of each +chunk/atom ` command. The number of columns is 4 for +the :math:`(x,y,z)` dipole vector components and the total dipole of each chunk. These values can be accessed by any command that uses global array values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The array values are "intensive". The array values will be in -dipole units, i.e. charge units times distance :doc:`units `. +The array values are "intensive." The array values will be in +dipole units (i.e., charge :doc:`units ` times distance +:doc:`units `). Restrictions """""""""""" diff --git a/doc/src/compute_displace_atom.rst b/doc/src/compute_displace_atom.rst index 688e73d914..1a99fd8e45 100644 --- a/doc/src/compute_displace_atom.rst +++ b/doc/src/compute_displace_atom.rst @@ -6,7 +6,7 @@ compute displace/atom command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID displace/atom @@ -35,9 +35,9 @@ atom in the group from its original (reference) coordinates, including all effects due to atoms passing through periodic boundaries. A vector of four quantities per atom is calculated by this compute. -The first 3 elements of the vector are the dx,dy,dz displacements. -The fourth component is the total displacement, i.e. sqrt(dx\*dx + dy\*dy + -dz\*dz). +The first three elements of the vector are the :math:`(dx,dy,dz)` +displacements. The fourth component is the total displacement +(i.e., :math:`\sqrt{dx^2 + dy^2 + dz^2}`). The displacement of an atom is from its original position at the time the compute command was issued. The value of the displacement will be @@ -50,7 +50,7 @@ the compute command was issued. The value of the displacement will be ` command for a discussion of "unwrapped" coordinates. See the Atoms section of the :doc:`read_data ` command for a discussion of image flags and how they are set for each atom. You - can reset the image flags (e.g. to 0) before invoking this compute + can reset the image flags (e.g., to 0) before invoking this compute by using the :doc:`set image ` command. .. note:: @@ -60,7 +60,7 @@ the compute command was issued. The value of the displacement will be you should use the same ID for this compute, as in the original run. This is so that the fix this compute creates to store per-atom quantities will also have the same ID, and thus be initialized - correctly with time=0 atom coordinates from the restart file. + correctly with time = 0 atom coordinates from the restart file. ---------- @@ -101,8 +101,8 @@ call to this compute at the end of every dump. The *refresh* argument for this compute is the ID of an :doc:`atom-style variable ` which calculates a Boolean value (0 or 1) based on the same criterion used by dump_modify thresh. This compute -evaluates the atom-style variable. For each atom that returns 1 -(true), the original (reference) coordinates of the atom (stored by +evaluates the atom-style variable. For each atom that returns 1 (true), +the original (reference) coordinates of the atom (stored by this compute) are updated. The effect of these commands is that a particular atom will only be @@ -125,8 +125,8 @@ would be empty. Output info """"""""""" -This compute calculates a per-atom array with 4 columns, which can be -accessed by indices 1-4 by any command that uses per-atom values from +This compute calculates a per-atom array with four columns, which can be +accessed by indices 1--4 by any command that uses per-atom values from a compute as input. See the :doc:`Howto output ` doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_dpd.rst b/doc/src/compute_dpd.rst index bc6e1d2321..16fa9279ff 100644 --- a/doc/src/compute_dpd.rst +++ b/doc/src/compute_dpd.rst @@ -6,7 +6,7 @@ compute dpd command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID dpd @@ -24,9 +24,9 @@ Description """"""""""" Define a computation that accumulates the total internal conductive -energy (:math:`U^{cond}`), the total internal mechanical energy -(:math:`U^{mech}`), the total chemical energy (:math:`U^{chem}`) -and the *harmonic* average of the internal temperature (:math:`\theta_{avg}`) +energy (:math:`U^{\text{cond}}`), the total internal mechanical energy +(:math:`U^{\text{mech}}`), the total chemical energy (:math:`U^\text{chem}`) +and the *harmonic* average of the internal temperature (:math:`\theta_\text{avg}`) for the entire system of particles. See the :doc:`compute dpd/atom ` command if you want per-particle internal energies and internal temperatures. @@ -36,22 +36,24 @@ relations: .. math:: - U^{cond} = & \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ - U^{mech} = & \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\ - U^{chem} = & \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\ - U = & \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\ - \theta_{avg} = & (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\ + U^\text{cond} = & \sum_{i=1}^{N} u_{i}^\text{cond} \\ + U^\text{mech} = & \sum_{i=1}^{N} u_{i}^\text{mech} \\ + U^\text{chem} = & \sum_{i=1}^{N} u_{i}^\text{chem} \\ + U = & \sum_{i=1}^{N} (u_{i}^\text{cond} + + u_{i}^\text{mech} + u_{i}^\text{chem}) \\ + \theta_{avg} = & \biggl(\frac{1}{N}\sum_{i=1}^{N} + \frac{1}{\theta_{i}}\biggr)^{-1} \\ -where :math:`N` is the number of particles in the system +where :math:`N` is the number of particles in the system. ---------- Output info """"""""""" -This compute calculates a global vector of length 5 (:math:`U^{cond}`, -:math:`U^{mech}`, :math:`U^{chem}`, :math:`\theta_{avg}`, :math:`N`), -which can be accessed by indices 1-5. +This compute calculates a global vector of length 5 (:math:`U^\text{cond}`, +:math:`U^\text{mech}`, :math:`U^\text{chem}`, :math:`\theta_\text{avg}`, +:math:`N`), which can be accessed by indices 1 through 5. See the :doc:`Howto output ` page for an overview of LAMMPS output options. @@ -61,7 +63,8 @@ Restrictions """""""""""" This command is part of the DPD-REACT package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +LAMMPS was built with that package. +See the :doc:`Build package ` page for more info. This command also requires use of the :doc:`atom_style dpd ` command. diff --git a/doc/src/compute_dpd_atom.rst b/doc/src/compute_dpd_atom.rst index 6104c4a273..7b38b8ff4f 100644 --- a/doc/src/compute_dpd_atom.rst +++ b/doc/src/compute_dpd_atom.rst @@ -6,7 +6,7 @@ compute dpd/atom command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID dpd/atom @@ -23,29 +23,28 @@ Examples Description """"""""""" -Define a computation that accesses the per-particle internal -conductive energy (:math:`u^{cond}`), internal mechanical -energy (:math:`u^{mech}`), internal chemical energy (:math:`u^{chem}`) -and internal temperatures (:math:`\theta`) for each particle in a group. +Define a computation that accesses the per-particle internal conductive energy +(:math:`u^\text{cond}`), internal mechanical energy (:math:`u^\text{mech}`), +internal chemical energy (:math:`u^\text{chem}`) and internal temperatures +(:math:`\theta`) for each particle in a group. See the :doc:`compute dpd ` command if you want the total internal conductive energy, the total internal mechanical energy, the -total chemical energy and -average internal temperature of the entire system or group of dpd -particles. +total chemical energy and average internal temperature of the entire system or +group of dpd particles. Output info """"""""""" -This compute calculates a per-particle array with 4 columns (:math:`u^{cond}`, -:math:`u^{mech}`, :math:`u^{chem}`, :math:`\theta`), which can be accessed -by indices 1-4 by any +This compute calculates a per-particle array with four columns +(:math:`u^\text{cond}`, :math:`u^\text{mech}`, :math:`u^\text{chem}`, +:math:`\theta`), which can be accessed by indices 1--4 by any command that uses per-particle values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The per-particle array values will be in energy (:math:`u^{cond}`, -:math:`u^{mech}`, :math:`u^{chem}`) -and temperature (:math:`theta`) :doc:`units `. +The per-particle array values will be in energy (:math:`u^\text{cond}`, +:math:`u^\text{mech}`, :math:`u^\text{chem}`) +and temperature (:math:`\theta`) :doc:`units `. Restrictions """""""""""" diff --git a/doc/src/compute_edpd_temp_atom.rst b/doc/src/compute_edpd_temp_atom.rst index 3568a6364f..d376511ec0 100644 --- a/doc/src/compute_edpd_temp_atom.rst +++ b/doc/src/compute_edpd_temp_atom.rst @@ -6,7 +6,7 @@ compute edpd/temp/atom command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID edpd/temp/atom diff --git a/doc/src/compute_efield_atom.rst b/doc/src/compute_efield_atom.rst index a3d2cb888d..1e63264b2a 100644 --- a/doc/src/compute_efield_atom.rst +++ b/doc/src/compute_efield_atom.rst @@ -6,12 +6,19 @@ compute efield/atom command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS - compute ID group-ID efield/atom + compute ID group-ID efield/atom keyword val * ID, group-ID are documented in :doc:`compute ` command * efield/atom = style name of this compute command +* zero or more keyword/value pairs may be appended +* keyword = *pair* or *kspace* + + .. parsed-literal:: + + *pair* args = *yes* or *no* + *kspace* args = *yes* or *no* Examples """""""" @@ -23,10 +30,10 @@ Examples Used in input scripts: - .. parsed-literal:: +.. parsed-literal:: - examples/PACKAGES/dielectric/in.confined - examples/PACKAGES/dielectric/in.nopbc + examples/PACKAGES/dielectric/in.confined + examples/PACKAGES/dielectric/in.nopbc Description """"""""""" diff --git a/doc/src/compute_entropy_atom.rst b/doc/src/compute_entropy_atom.rst index e3d585dfde..f733c00f97 100644 --- a/doc/src/compute_entropy_atom.rst +++ b/doc/src/compute_entropy_atom.rst @@ -6,14 +6,14 @@ compute entropy/atom command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID entropy/atom sigma cutoff keyword value ... * ID, group-ID are documented in :doc:`compute ` command * entropy/atom = style name of this compute command -* sigma = width of gaussians used in the g(r) smoothing -* cutoff = cutoff for the g(r) calculation +* sigma = width of Gaussians used in the :math:`g(r)` smoothing +* cutoff = cutoff for the :math:`g(r)` calculation * one or more keyword/value pairs may be appended .. parsed-literal:: @@ -53,31 +53,32 @@ This parameter for atom i is computed using the following formula from s_S^i=-2\pi\rho k_B \int\limits_0^{r_m} \left [ g(r) \ln g(r) - g(r) + 1 \right ] r^2 dr -where r is a distance, g(r) is the radial distribution function of atom -i and rho is the density of the system. The g(r) computed for each -atom i can be noisy and therefore it is smoothed using: +where :math:`r` is a distance, :math:`g(r)` is the radial distribution function +of atom :math:`i`, and :math:`\rho` is the density of the system. +The :math:`g(r)` computed for each atom :math:`i` can be noisy and therefore it +is smoothed using .. math:: g_m^i(r) = \frac{1}{4 \pi \rho r^2} \sum\limits_{j} \frac{1}{\sqrt{2 \pi \sigma^2}} e^{-(r-r_{ij})^2/(2\sigma^2)} -where the sum in j goes through the neighbors of atom i, and :math:`\sigma` -is a parameter to control the smoothing. +where the sum over :math:`j` goes through the neighbors of atom :math:`i` and +:math:`\sigma` is a parameter to control the smoothing. The input parameters are *sigma* the smoothing parameter :math:`\sigma`, -and the *cutoff* for the calculation of g(r). +and the *cutoff* for the calculation of :math:`g(r)`. If the keyword *avg* has the setting *yes*, then this compute also -averages the parameter over the neighbors of atom i according to: +averages the parameter over the neighbors of atom :math:`i` according to .. math:: - \left< s_S^i \right> = \frac{\sum_j s_S^j + s_S^i}{N + 1} + \left< s_S^i \right> = \frac{\sum_j s_S^j + s_S^i}{N + 1}, -where the sum j goes over the neighbors of atom i and N is the number -of neighbors. This procedure provides a sharper distinction between -order and disorder environments. In this case the input parameter -*cutoff2* is the cutoff for the averaging over the neighbors and +where the sum over :math:`j` goes over the neighbors of atom :math:`i` and +:math:`N` is the number of neighbors. This procedure provides a sharper +distinction between order and disorder environments. In this case the input +parameter *cutoff2* is the cutoff for the averaging over the neighbors and must also be specified. If the *avg yes* option is used, the effective cutoff of the neighbor @@ -90,20 +91,20 @@ to increase the skin of the neighbor list with: See :doc:`neighbor ` for details. -If the *local yes* option is used, the g(r) is normalized by the +If the *local yes* option is used, the :math:`g(r)` is normalized by the local density around each atom, that is to say the density around each atom is the number of neighbors within the neighbor list cutoff divided 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 4.05 Angstroms), +constant 4.05 Ångströms), .. 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 4.23 Ångströms), .. parsed-literal:: @@ -114,7 +115,8 @@ Output info By default, this compute calculates the pair entropy value for each atom as a per-atom vector, which can be accessed by any command that -uses per-atom values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output +uses per-atom values from a compute as input. See the +:doc:`Howto output ` page for an overview of LAMMPS output options. The pair entropy values have units of the Boltzmann constant. They are diff --git a/doc/src/compute_erotate_asphere.rst b/doc/src/compute_erotate_asphere.rst index 2b4edc8017..44415c63cc 100644 --- a/doc/src/compute_erotate_asphere.rst +++ b/doc/src/compute_erotate_asphere.rst @@ -6,7 +6,7 @@ compute erotate/asphere command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID erotate/asphere @@ -30,9 +30,9 @@ ellipsoids, or line segments, or triangles. See the for descriptions of these options. For all 3 types of particles, the rotational kinetic energy is -computed as 1/2 I w\^2, where I is the inertia tensor for the -aspherical particle and w is its angular velocity, which is computed -from its angular momentum if needed. +computed as :math:`\frac12 I \omega^2`, where :math:`I` is the inertia tensor +for the aspherical particle and :math:`\omega` is its angular velocity, which +is computed from its angular momentum if needed. .. note:: @@ -48,7 +48,7 @@ used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive". The +The scalar value calculated by this compute is "extensive." The scalar value will be in energy :doc:`units `. Restrictions @@ -65,7 +65,7 @@ This compute requires that triangular particles atoms store a size and shape and quaternion orientation and angular momentum as defined by the :doc:`atom_style tri ` command. -All particles in the group must be finite-size. They cannot be point +All particles in the group must be of finite size. They cannot be point particles. Related commands diff --git a/doc/src/compute_erotate_rigid.rst b/doc/src/compute_erotate_rigid.rst index acbcf5cb0c..1e03a2316c 100644 --- a/doc/src/compute_erotate_rigid.rst +++ b/doc/src/compute_erotate_rigid.rst @@ -6,7 +6,7 @@ compute erotate/rigid command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID erotate/rigid fix-ID @@ -25,18 +25,20 @@ Description """"""""""" Define a computation that calculates the rotational kinetic energy of -a collection of rigid bodies, as defined by one of the :doc:`fix rigid ` command variants. +a collection of rigid bodies, as defined by one of the +:doc:`fix rigid ` command variants. -The rotational energy of each rigid body is computed as 1/2 I Wbody\^2, -where I is the inertia tensor for the rigid body, and Wbody is its -angular velocity vector. Both I and Wbody are in the frame of -reference of the rigid body, i.e. I is diagonalized. +The rotational energy of each rigid body is computed as +:math:`\frac12 I \omega_\text{body}^2`, +where :math:`I` is the inertia tensor for the rigid body and +:math:`\omega_\text{body}` is its angular velocity vector. +Both :math:`I` and :math:`\omega_\text{body}` are in the frame of +reference of the rigid body (i.e., :math:`I` is diagonal). The *fix-ID* should be the ID of one of the :doc:`fix rigid ` commands which defines the rigid bodies. The group specified in the compute command is ignored. The rotational energy of all the rigid -bodies defined by the fix rigid command in included in the -calculation. +bodies defined by the fix rigid command in included in the calculation. Output info """"""""""" @@ -46,14 +48,15 @@ of all the rigid bodies). This value can be used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive". The +The scalar value calculated by this compute is "extensive." The scalar value will be in energy :doc:`units `. Restrictions """""""""""" This compute is part of the RIGID package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +LAMMPS was built with that package. See the +:doc:`Build package ` page for more info. Related commands """""""""""""""" diff --git a/doc/src/compute_erotate_sphere.rst b/doc/src/compute_erotate_sphere.rst index 6890f18212..28b0052b89 100644 --- a/doc/src/compute_erotate_sphere.rst +++ b/doc/src/compute_erotate_sphere.rst @@ -6,7 +6,7 @@ compute erotate/sphere command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID erotate/sphere @@ -26,8 +26,9 @@ Description Define a computation that calculates the rotational kinetic energy of a group of spherical particles. -The rotational energy is computed as 1/2 I w\^2, where I is the moment -of inertia for a sphere and w is the particle's angular velocity. +The rotational energy is computed as :math:`\frac12 I \omega^2`, +where :math:`I` is the moment of inertia for a sphere and :math:`\omega` +is the particle's angular velocity. .. note:: @@ -43,7 +44,7 @@ used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "extensive". The +The scalar value calculated by this compute is "extensive." The scalar value will be in energy :doc:`units `. Restrictions diff --git a/doc/src/compute_erotate_sphere_atom.rst b/doc/src/compute_erotate_sphere_atom.rst index 76025b36f7..611cd83c01 100644 --- a/doc/src/compute_erotate_sphere_atom.rst +++ b/doc/src/compute_erotate_sphere_atom.rst @@ -6,7 +6,7 @@ compute erotate/sphere/atom command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID erotate/sphere/atom @@ -26,8 +26,9 @@ Description Define a computation that calculates the rotational kinetic energy for each particle in a group. -The rotational energy is computed as 1/2 I w\^2, where I is the moment -of inertia for a sphere and w is the particle's angular velocity. +The rotational energy is computed as :math:`\frac12 I \omega^2`, where +:math:`I` is the moment of inertia for a sphere and :math:`\omega` is the +particle's angular velocity. .. note:: @@ -36,8 +37,7 @@ of inertia for a sphere and w is the particle's angular velocity. as in 3d. The value of the rotational kinetic energy will be 0.0 for atoms not -in the specified compute group or for point particles with a radius = -0.0. +in the specified compute group or for point particles with a radius of 0.0. Output info """"""""""" diff --git a/doc/src/compute_event_displace.rst b/doc/src/compute_event_displace.rst index 6cf04e83ba..f8911e1224 100644 --- a/doc/src/compute_event_displace.rst +++ b/doc/src/compute_event_displace.rst @@ -6,7 +6,7 @@ compute event/displace command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID event/displace threshold @@ -27,10 +27,9 @@ Description Define a computation that flags an "event" if any particle in the group has moved a distance greater than the specified threshold distance when compared to a previously stored reference state -(i.e. the previous event). This compute is typically used in +(i.e., the previous event). This compute is typically used in conjunction with the :doc:`prd ` and :doc:`tad ` commands, -to detect if a transition -to a new minimum energy basin has occurred. +to detect if a transition to a new minimum energy basin has occurred. This value calculated by the compute is equal to 0 if no particle has moved far enough, and equal to 1 if one or more particles have moved @@ -51,7 +50,7 @@ used by any command that uses a global scalar value from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. -The scalar value calculated by this compute is "intensive". The +The scalar value calculated by this compute is "intensive." The scalar value will be a 0 or 1 as explained above. Restrictions diff --git a/doc/src/compute_fabric.rst b/doc/src/compute_fabric.rst index 3ded3d7adc..b454e67729 100644 --- a/doc/src/compute_fabric.rst +++ b/doc/src/compute_fabric.rst @@ -6,7 +6,7 @@ compute fabric command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID fabric cutoff attribute1 attribute2 ... keyword values ... @@ -63,7 +63,7 @@ tangential force tensor. The contact tensor is calculated as .. math:: - C_{ab} = \frac{15}{2} (\phi_{ab} - \mathrm{tr}(\phi) \delta_{ab}) + C_{ab} = \frac{15}{2} (\phi_{ab} - \mathrm{Tr}(\phi) \delta_{ab}) where :math:`a` and :math:`b` are the :math:`x`, :math:`y`, :math:`z` directions, :math:`\delta_{ab}` is the Kronecker delta function, and @@ -75,13 +75,14 @@ the tensor :math:`\phi` is defined as where :math:`n` loops over the :math:`N_p` pair interactions in the simulation, :math:`r_{a}` is the :math:`a` component of the radial vector between the -two pairwise interacting particles, and :math:`r` is the magnitude of the radial vector. +two pairwise interacting particles, and :math:`r` is the magnitude of the +radial vector. The branch tensor is calculated as .. math:: - B_{ab} = \frac{15}{6 \mathrm{tr}(D)} (D_{ab} - \mathrm{tr}(D) \delta_{ab}) + B_{ab} = \frac{15}{6 \mathrm{Tr}(D)} (D_{ab} - \mathrm{Tr}(D) \delta_{ab}) where the tensor :math:`D` is defined as @@ -91,14 +92,15 @@ where the tensor :math:`D` is defined as \frac{1}{N_c (r^2 + C_{cd} r_c r_d)} \frac{r_{a} r_{b}}{r} -where :math:`N_c` is the total number of contacts in the system and the subscripts -:math:`c` and :math:`d` indices are summed according to Einstein notation. +where :math:`N_c` is the total number of contacts in the system and the +subscripts :math:`c` and :math:`d` indices are summed according to Einstein +notation. The normal force fabric tensor is calculated as .. math:: - F^n_{ab} = \frac{15}{6 \mathrm{tr}(N)} (N_{ab} - \mathrm{tr}(N) \delta_{ab}) + F^n_{ab} = \frac{15}{6\, \mathrm{Tr}(N)} (N_{ab} - \mathrm{Tr}(N) \delta_{ab}) where the tensor :math:`N` is defined as @@ -116,7 +118,7 @@ as .. math:: - F^t_{ab} = \frac{15}{9 \mathrm{tr}(N)} (T_{ab} - \mathrm{tr}(T) \delta_{ab}) + F^t_{ab} = \frac{15}{9\, \mathrm{Tr}(N)} (T_{ab} - \mathrm{Tr}(T) \delta_{ab}) where the tensor :math:`T` is defined as @@ -133,21 +135,23 @@ Interactions between two atoms are only included in calculations if the atom typ are in the two lists. Each list consists of a series of type ranges separated by commas. The range can be specified as a single numeric value, or a wildcard asterisk can be used to specify a range -of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For -example, if M = the number of atom types, then an asterisk with no numeric -values means all types from 1 to M. A leading asterisk means all types -from 1 to n (inclusive). A trailing asterisk means all types from n to M -(inclusive). A middle asterisk means all types from m to n (inclusive). -Multiple *type/include* keywords may be added. +of values. This takes the form "\*" or "\*n" or "m\*" or "m\*n". For +example, if :math:`M` is the number of atom types, then an asterisk with no +numeric values means all types from 1 to :math:`M`. A leading asterisk means +all types from 1 to n (inclusive). A trailing asterisk means all types from +m to :math:`M` (inclusive). A middle asterisk means all types from m to n +(inclusive). Multiple *type/include* keywords may be added. Output info """"""""""" -This compute calculates a local vector of doubles and a scalar. The vector stores the -unique components of the first requested tensor in the order xx, yy, zz, xy, xz, yz -followed by the same components for all subsequent tensors. The length of the vector -is therefore six times the number of requested tensors. The scalar output is the -number of pairwise interactions included in the calculation of the fabric tensor. +This compute calculates a local vector of doubles and a scalar. The vector +stores the unique components of the first requested tensor in the order +:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz` +followed by the same components for all subsequent tensors. +The length of the vector is therefore six times the number of requested +tensors. The scalar output is the number of pairwise interactions included in +the calculation of the fabric tensor. Restrictions """""""""""" @@ -164,7 +168,7 @@ following fixes which add rigid-body constraints: :doc:`fix shake `, :doc:`fix rattle `, :doc:`fix rigid `, :doc:`fix rigid/small `. It does not support granular pair styles that extend beyond the contact of atomic radii -(e.g. JKR and DMT). +(e.g., JKR and DMT). Related commands """""""""""""""" diff --git a/doc/src/compute_fep.rst b/doc/src/compute_fep.rst index 5275716c45..b31fce5430 100644 --- a/doc/src/compute_fep.rst +++ b/doc/src/compute_fep.rst @@ -6,7 +6,7 @@ compute fep command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID fep temp attribute args ... keyword value ... @@ -19,7 +19,7 @@ Syntax .. parsed-literal:: *pair* args = pstyle pparam I J v_delta - pstyle = pair style name, e.g. lj/cut + pstyle = pair style name (e.g., *lj/cut*) pparam = parameter to perturb I,J = type pair(s) to set parameter for v_delta = variable with perturbation to apply (in the units of the parameter) @@ -37,8 +37,8 @@ Syntax *no* = ignore tail correction to pair energies (usually small in fep) *yes* = include tail correction to pair energies *volume* value = *no* or *yes* - *no* = ignore volume changes (e.g. in *NVE* or *NVT* trajectories) - *yes* = include volume changes (e.g. in *NpT* trajectories) + *no* = ignore volume changes (e.g., in *NVE* or *NVT* trajectories) + *yes* = include volume changes (e.g., in *NPT* trajectories) Examples """""""" @@ -84,7 +84,7 @@ It is possible but not necessary that the coupling parameter (or a function thereof) appears as a multiplication factor of the potential energy. Therefore, this compute can apply perturbations to interaction parameters that are not directly proportional to the potential energy -(e.g. :math:`\sigma` in Lennard-Jones potentials). +(e.g., :math:`\sigma` in Lennard-Jones potentials). This command can be combined with :doc:`fix adapt ` to perform multistage free-energy perturbation calculations along @@ -107,7 +107,8 @@ perturbation method using a very small :math:`\delta`: A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda \approx \sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) - A(\lambda_i)}{\delta} -where :math:`w_i` are weights of a numerical quadrature. The :doc:`fix adapt ` command can be used to define the stages of +where :math:`w_i` are weights of a numerical quadrature. The +:doc:`fix adapt ` command can be used to define the stages of :math:`\lambda` at which the derivative is calculated and averaged. The compute fep calculates the exponential Boltzmann term and also the @@ -125,7 +126,7 @@ the derivative of the potential energy with respect to :math:`\lambda`: Another technique to calculate free energy differences is the acceptance ratio method :ref:`(Bennet) `, which can be implemented -by calculating the potential energy differences with :math:`\delta` = 1.0 on +by calculating the potential energy differences with :math:`\delta = 1.0` on both the forward and reverse routes: .. math:: @@ -226,17 +227,17 @@ the pair\_\*.cpp file associated with the potential. Similar to the :doc:`pair_coeff ` command, I and J can be specified in one of two ways. Explicit numeric values can be used for -each, as in the first example above. I <= J is required. LAMMPS sets +each, as in the first example above. I :math:`\le` J is required. LAMMPS sets the coefficients for the symmetric J,I interaction to the same values. A wild-card asterisk can be used in place of or in conjunction with the I,J arguments to set the coefficients for multiple pairs of -atom types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = -the number of atom types, then an asterisk with no numeric values -means all types from 1 to N. A leading asterisk means all types from -1 to n (inclusive). A trailing asterisk means all types from n to N +atom types. This takes the form "\*" or "\*n" or "m\*" or "m\*n". If +:math:`N` is the number of atom types, then an asterisk with no numeric values +means all types from 1 to :math:`N`. A leading asterisk means all types from +1 to n (inclusive). A trailing asterisk means all types from m to N (inclusive). A middle asterisk means all types from m to n -(inclusive). Note that only type pairs with I <= J are considered; if -asterisks imply type pairs where J < I, they are ignored. +(inclusive). Note that only type pairs with I :math:`\le` J are considered; if +asterisks imply type pairs where J :math:`<` I, they are ignored. If :doc:`pair_style hybrid or hybrid/overlay ` is being used, then the *pstyle* will be a sub-style name. You must specify @@ -298,7 +299,7 @@ These output results can be used by any command that uses a global scalar or vector from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output options. For example, the computed values can be averaged using :doc:`fix ave/time `. -The values calculated by this compute are "extensive". +The values calculated by this compute are "extensive." Restrictions """""""""""" diff --git a/doc/src/compute_fep_ta.rst b/doc/src/compute_fep_ta.rst index eeb4a10915..504ed6aa23 100644 --- a/doc/src/compute_fep_ta.rst +++ b/doc/src/compute_fep_ta.rst @@ -6,7 +6,7 @@ compute fep/ta command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID fep/ta temp plane scale_factor keyword value ... @@ -20,9 +20,9 @@ Syntax .. parsed-literal:: - *tail* value = *no* or *yes* - *no* = ignore tail correction to pair energies (usually small in fep) - *yes* = include tail correction to pair energies + *tail* value = *no* or *yes* + *no* = ignore tail correction to pair energies (usually small in fep) + *yes* = include tail correction to pair energies Examples """""""" @@ -42,11 +42,12 @@ in a single simulation: .. math:: \gamma = \lim_{\Delta \mathcal{A} \to 0} \left( \frac{\Delta A_{0 \to 1 }}{\Delta \mathcal{A}}\right)_{N,V,T} - = - \frac{kT}{\Delta \mathcal{A}} \ln \left< \exp(-(U_1 - U_0)/kT) \right>_0 + = - \frac{kT}{\Delta \mathcal{A}} \ln \left\langle \exp\left(\frac{-(U_1 - U_0)}{kT}\right) \right\rangle_0 During the perturbation, both axes of *plane* are scaled by multiplying -:math:`\sqrt{scale\_factor}`, while the other axis divided by -*scale_factor* such that the overall volume of the system is maintained. +:math:`\sqrt{\mathrm{scale\_factor}}`, while the other axis divided by +:math:`\mathrm{scale\_factor}` such that the overall volume of the system is +maintained. The *tail* keyword controls the calculation of the tail correction to "van der Waals" pair energies beyond the cutoff, if this has been @@ -60,8 +61,8 @@ Output info """"""""""" This compute calculates a global vector of length 3 which contains the -energy difference ( :math:`U_1-U_0` ) as c_ID[1], the Boltzmann factor -:math:`\exp(-(U_1-U_0)/kT)`, as c_ID[2] and the change in the *plane* +energy difference :math:`(U_1-U_0)` as c_ID[1], the Boltzmann factor +:math:`\exp\bigl(-(U_1-U_0)/kT\bigr)`, as c_ID[2] and the change in the *plane* area :math:`\Delta \mathcal{A}` as c_ID[3]. :math:`U_1` is the potential energy of the perturbed state and :math:`U_0` is the potential energy of the reference state. The energies include kspace terms if these are diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst index 47f8c5da48..fd979d19a0 100644 --- a/doc/src/compute_tally.rst +++ b/doc/src/compute_tally.rst @@ -26,7 +26,7 @@ compute stress/tally command Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID style group2-ID @@ -57,8 +57,8 @@ accumulated directly during the non-bonded force computation. The computes *force/tally*, *pe/tally*, *stress/tally*, and *heat/flux/tally* are primarily provided as example how to program additional, more sophisticated computes using the tally callback -mechanism. Compute *pe/mol/tally* is one such style, that can -- through using this mechanism - separately tally intermolecular +mechanism. Compute *pe/mol/tally* is one such style, that can---through using +this mechanism---separately tally intermolecular and intramolecular energies. Something that would otherwise be impossible without integrating this as a core functionality into the base classes of LAMMPS. @@ -92,7 +92,7 @@ Although, the *heat/flux/virial/tally* compute does not include the convective term, it can be used to obtain the total heat flux over control surfaces, when there are no particles crossing over, -such as is often in solid-solid and solid-liquid interfaces. +such as is often in solid--solid and solid--liquid interfaces. This would be identical to the method of planes method. Note that the *heat/flux/virial/tally* compute is distinctly different from the *heat/flux* and *heat/flux/tally* computes, @@ -152,7 +152,7 @@ Output info atom scalar (the contributions of the single atom to the global scalar). -- Compute *pe/mol/tally* calculates a global 4-element vector containing +- Compute *pe/mol/tally* calculates a global four-element vector containing (in this order): *evdwl* and *ecoul* for intramolecular pairs and *evdwl* and *ecoul* for intermolecular pairs. Since molecules are identified by their molecule IDs, the partitioning does not have to be @@ -165,24 +165,24 @@ Output info - Compute *stress/tally* calculates a global scalar (average of the diagonal elements of the stress tensor) and a per atom - vector (the 6 elements of stress tensor contributions from the + vector (the six elements of stress tensor contributions from the individual atom). - As in :doc:`compute heat/flux `, compute *heat/flux/tally* calculates a global vector of length 6, - where the first 3 components are the :math:`x`, :math:`y`, :math:`z` + where the first three components are the :math:`x`, :math:`y`, :math:`z` components of the full heat flow vector, - and the next 3 components are the corresponding components - of just the convective portion of the flow, i.e. the - first term in the equation for :math:`\mathbf{Q}`. + and the next three components are the corresponding components + of just the convective portion of the flow (i.e., the + first term in the equation for :math:`\mathbf{Q}`). - Compute *heat/flux/virial/tally* calculates a global scalar (heat flow) - and a per atom 3-element vector + and a per atom three-element vector (contribution to the force acting over atoms in the first group from individual atoms in both groups). Both the scalar and vector values calculated by this compute are -"extensive". +"extensive." Restrictions """"""""""""