See Section 6.10 of the manual and
the couple directory of the distribution for more ideas about coupling
-LAMMPS to other codes. See Section_howto 19 for a description of the LAMMPS
+LAMMPS to other codes. See Section 6.19 for a description of the LAMMPS
library interface provided in src/library.cpp and src/library.h, and
how to extend it for your needs. As described below, that interface
is what is exposed to Python either when calling LAMMPS from Python or
diff --git a/doc/html/Section_start.html b/doc/html/Section_start.html
index f01f969f79..bc1af70cda 100644
--- a/doc/html/Section_start.html
+++ b/doc/html/Section_start.html
@@ -1258,7 +1258,7 @@ manual. See
The files src/library.cpp and library.h define the C-style API for
-using LAMMPS as a library. See Section_howto 19 of the manual for a description of the
+using LAMMPS as a library. See Section 6.19 of the manual for a description of the
interface and how to extend it for your needs.
diff --git a/doc/html/atom_style.html b/doc/html/atom_style.html
index 0ec90b2ce3..21aa1f2d52 100644
--- a/doc/html/atom_style.html
+++ b/doc/html/atom_style.html
@@ -283,7 +283,7 @@ output the custom values.
All of the above styles define point particles, except the sphere, ellipsoid, electron, peri, wavepacket, line, tri, and -body styles, which define finite-size particles. See Section_howto 14 for an overview of using finite-size +body styles, which define finite-size particles. See Section 6.14 for an overview of using finite-size particle models with LAMMPS.
All of the point-particle styles assign mass to particles on a per-type basis, using the mass command, The finite-size diff --git a/doc/html/compute_angmom_chunk.html b/doc/html/compute_angmom_chunk.html index 88bb01d89f..619b229f3b 100644 --- a/doc/html/compute_angmom_chunk.html +++ b/doc/html/compute_angmom_chunk.html @@ -150,7 +150,7 @@ chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for 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 3 components of the angular momentum @@ -188,7 +188,7 @@ fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = 3 for the 3 xyz components of the angular momentum for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +values from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The array values are “intensive”. The array values will be in mass-velocity-distance units.
diff --git a/doc/html/compute_basal_atom.html b/doc/html/compute_basal_atom.html index 683fcf61d0..fe4f20db0e 100644 --- a/doc/html/compute_basal_atom.html +++ b/doc/html/compute_basal_atom.html @@ -163,7 +163,7 @@ in examples/USER/misc/basal.Output info:
This compute calculates a per-atom array with 3 columns, which can be accessed by indices 1-3 by any command that uses per-atom values from -a compute as input. See Section_howto 15 for an overview of LAMMPS output +a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The per-atom vector values are unitless since the 3 columns represent components of a unit vector.
diff --git a/doc/html/compute_centro_atom.html b/doc/html/compute_centro_atom.html index 5b1779546e..bb862d687a 100644 --- a/doc/html/compute_centro_atom.html +++ b/doc/html/compute_centro_atom.html @@ -212,7 +212,7 @@ too frequently or to have multiple compute/dump commands, each with aOutput info:
By default, this compute calculates the centrosymmetry 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 Section_howto 15 for an overview of LAMMPS output +uses per-atom values from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
If the axes keyword setting is yes, then a per-atom array is calculated. The first column is the centrosymmetry parameter. The diff --git a/doc/html/compute_chunk_atom.html b/doc/html/compute_chunk_atom.html index 817d511170..cf45a9f2a2 100644 --- a/doc/html/compute_chunk_atom.html +++ b/doc/html/compute_chunk_atom.html @@ -224,7 +224,7 @@ another comp computes with “chunk” in their style name, such as compute com/chunk or compute msd/chunk. Or they can be used by the fix ave/chunk command to sum and time average a variety of per-atom properties over the atoms in each chunk. Or they can simply be accessed by any command that uses per-atom values from a -compute as input, as discussed in Section_howto 15.
+compute as input, as discussed in Section 6.15.See Section 6.23 for an overview of how this compute can be used with a variety of other commands to tabulate properties of a simulation. The howto section gives several diff --git a/doc/html/compute_com_chunk.html b/doc/html/compute_com_chunk.html index e2bce3f872..87dbed66a3 100644 --- a/doc/html/compute_com_chunk.html +++ b/doc/html/compute_com_chunk.html @@ -150,7 +150,7 @@ chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for 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 center-of-mass @@ -186,7 +186,7 @@ fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = 3 for the 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 Section_howto 15 for an overview of LAMMPS output +from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The array values are “intensive”. The array values will be in distance units.
diff --git a/doc/html/compute_coord_atom.html b/doc/html/compute_coord_atom.html index 67663e1ce2..35a778e631 100644 --- a/doc/html/compute_coord_atom.html +++ b/doc/html/compute_coord_atom.html @@ -194,7 +194,7 @@ the neighbor list. this compute calculates a per-atom vector. If multiple typeN keywords are specified, this compute calculates a per-atom array, with N columns. These values can be accessed by any command that uses -per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +per-atom values from a compute as input. See Section 6.15 for an overview of LAMMPS output options.The per-atom vector or array values will be a number >= 0.0, as explained above.
diff --git a/doc/html/compute_dipole_chunk.html b/doc/html/compute_dipole_chunk.html index efedfa0512..4a16b859c8 100644 --- a/doc/html/compute_dipole_chunk.html +++ b/doc/html/compute_dipole_chunk.html @@ -152,7 +152,7 @@ for multiple chunks of atoms.In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for 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 @@ -191,7 +191,7 @@ fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = 4 for the 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 Section_howto 15 for an overview of LAMMPS output +array values from a compute as input. See Section 6.15 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 units.
diff --git a/doc/html/compute_displace_atom.html b/doc/html/compute_displace_atom.html index 14b3b05284..7cded17a76 100644 --- a/doc/html/compute_displace_atom.html +++ b/doc/html/compute_displace_atom.html @@ -175,7 +175,7 @@ correctly with time=0 atom coordinates from the restart file.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 -a compute as input. See Section_howto 15 for an overview of LAMMPS output +a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The per-atom array values will be in distance units.
diff --git a/doc/html/compute_dpd_atom.html b/doc/html/compute_dpd_atom.html index ef2c8dedf7..e3bbb3c7cc 100644 --- a/doc/html/compute_dpd_atom.html +++ b/doc/html/compute_dpd_atom.html @@ -155,7 +155,7 @@ particles.This compute calculates a per-particle array with 4 columns (u_cond, u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command that uses per-particle values from a compute as input. See -Section_howto15 for an overview of +Section 6.15 for an overview of LAMMPS output options.
The per-particle array values will be in energy (u_cond, u_mech, u_chem) and temperature (dpdTheta) units.
diff --git a/doc/html/compute_fep.html b/doc/html/compute_fep.html index 0824a98ae4..982fd70978 100644 --- a/doc/html/compute_fep.html +++ b/doc/html/compute_fep.html @@ -355,7 +355,7 @@ pair potential energy obtained with the perturbed parameters and unperturbed parameters. The energies include kspace terms if these are used in the simulation.These output results can be used by any command that uses a global -scalar or vector from a compute as input. See Section_howto 15 for an overview of LAMMPS output +scalar or vector from a compute as input. See Section 6.15 for an overview of LAMMPS output options. For example, the computed values can be averaged using fix ave/time.
The values calculated by this compute are “extensive”.
diff --git a/doc/html/compute_gyration.html b/doc/html/compute_gyration.html index 9d92b09b0d..ce2d468094 100644 --- a/doc/html/compute_gyration.html +++ b/doc/html/compute_gyration.html @@ -173,7 +173,7 @@ using the set imThis compute calculates a global scalar (Rg) and a global vector of length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These values can be used by any command that uses a global scalar value or -vector values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +vector values from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The scalar and vector values calculated by this compute are “intensive”. The scalar and vector values will be in distance and diff --git a/doc/html/compute_gyration_chunk.html b/doc/html/compute_gyration_chunk.html index 3ec0dca379..71d868cd8e 100644 --- a/doc/html/compute_gyration_chunk.html +++ b/doc/html/compute_gyration_chunk.html @@ -156,7 +156,7 @@ multiple chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for 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 radius of gyration Rg for each chunk, diff --git a/doc/html/compute_hexorder_atom.html b/doc/html/compute_hexorder_atom.html index 7f7ef8f450..da55aa52d0 100644 --- a/doc/html/compute_hexorder_atom.html +++ b/doc/html/compute_hexorder_atom.html @@ -211,7 +211,7 @@ the neighbor list.
real and imaginary parts qn, a complex number restricted to the unit disk of the complex plane i.e. Re(qn)^2 + Im(qn)^2 <= 1 .These values can be accessed by any command that uses -per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +per-atom values from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for 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 6 components of the symmetric intertia @@ -187,7 +187,7 @@ fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = 6 for the 6 components of the inertia tensor for each chunk, ordered as listed above. These values can be accessed by any command that -uses global array values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +uses global array values from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The array values are “intensive”. The array values will be in mass*distance^2 units.
diff --git a/doc/html/compute_ke_rigid.html b/doc/html/compute_ke_rigid.html index 27c5451b25..36653ade51 100644 --- a/doc/html/compute_ke_rigid.html +++ b/doc/html/compute_ke_rigid.html @@ -158,7 +158,7 @@ calculation.Output info:
This compute calculates a global scalar (the summed KE 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 Section_howto 15 for an overview of LAMMPS output +global scalar value from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The scalar value calculated by this compute is “extensive”. The scalar value will be in energy units.
diff --git a/doc/html/compute_msd_chunk.html b/doc/html/compute_msd_chunk.html index 2ef599ab24..024d81682e 100644 --- a/doc/html/compute_msd_chunk.html +++ b/doc/html/compute_msd_chunk.html @@ -150,7 +150,7 @@In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system.
Four quantites are calculated by this compute for each chunk. The diff --git a/doc/html/compute_omega_chunk.html b/doc/html/compute_omega_chunk.html index cb2e600901..a2c9a05117 100644 --- a/doc/html/compute_omega_chunk.html +++ b/doc/html/compute_omega_chunk.html @@ -150,7 +150,7 @@ multiple chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for 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 3 components of the angular velocity @@ -188,7 +188,7 @@ fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = 3 for the 3 xyz components of the angular velocity for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +values from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The array values are “intensive”. The array values will be in velocity/distance units.
diff --git a/doc/html/compute_orientorder_atom.html b/doc/html/compute_orientorder_atom.html index f3d10f42e9..d4ac7d41d2 100644 --- a/doc/html/compute_orientorder_atom.html +++ b/doc/html/compute_orientorder_atom.html @@ -214,7 +214,7 @@ the neighbor list.This compute calculates a per-atom array with nlvalues columns, giving the Ql values for each atom, which are real numbers on the range 0 <= Ql <= 1.
These values can be accessed by any command that uses -per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +per-atom values from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
Output info:
This compute calculates a global scalar (the potential energy). This value can be used by any command that uses a global scalar value from -a compute as input. See Section_howto 15 for an overview of LAMMPS output +a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The scalar value calculated by this compute is “extensive”. The scalar value will be in energy units.
diff --git a/doc/html/compute_property_chunk.html b/doc/html/compute_property_chunk.html index 7cf73b649d..9f1abcd413 100644 --- a/doc/html/compute_property_chunk.html +++ b/doc/html/compute_property_chunk.html @@ -157,7 +157,7 @@ atoms.In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system.
This compute calculates and stores the specified attributes of chunks diff --git a/doc/html/compute_smd_ulsph_strain_rate.html b/doc/html/compute_smd_ulsph_strain_rate.html index 0f60ae8efd..239ca65168 100644 --- a/doc/html/compute_smd_ulsph_strain_rate.html +++ b/doc/html/compute_smd_ulsph_strain_rate.html @@ -152,7 +152,7 @@ Mach Dynamics in LAMMPS.
Output info:
This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See Section_howto 15 for an overview of LAMMPS output +from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The values will be given in units of one over time.
The per-particle vector has 6 entries, corresponding to the xx, yy, diff --git a/doc/html/compute_smd_ulsph_stress.html b/doc/html/compute_smd_ulsph_stress.html index 51654a43e0..9d4e7e9dfc 100644 --- a/doc/html/compute_smd_ulsph_stress.html +++ b/doc/html/compute_smd_ulsph_stress.html @@ -150,7 +150,7 @@ Mach Dynamics in LAMMPS.
Output info:
This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See Section_howto 15 for an overview of LAMMPS output +from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The values will be given in units of pressure.
The per-particle vector has 7 entries. The first six entries diff --git a/doc/html/compute_sna_atom.html b/doc/html/compute_sna_atom.html index 930f66a12e..f950494367 100644 --- a/doc/html/compute_sna_atom.html +++ b/doc/html/compute_sna_atom.html @@ -305,7 +305,7 @@ block contains six sub-blocks corresponding to the xx, yy, sna/atom
These values can be accessed by any command that uses per-atom values -from a compute as input. See Section_howto 15 for an overview of LAMMPS output +from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
Output info:
This compute calculates a per-atom array with 6 columns, which can be accessed by indices 1-6 by any command that uses per-atom values from -a compute as input. See Section_howto 15 for an overview of LAMMPS output +a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The per-atom array values will be in pressure*volume units as discussed above.
diff --git a/doc/html/compute_temp_chunk.html b/doc/html/compute_temp_chunk.html index 88aba84049..54f3ec1be0 100644 --- a/doc/html/compute_temp_chunk.html +++ b/doc/html/compute_temp_chunk.html @@ -177,7 +177,7 @@ multiple chunks of atoms.In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system.
The temperature is calculated by the formula KE = DOF/2 k T, where KE = @@ -308,7 +308,7 @@ of the optional values are specified. The number of rows in the array compute chunk/atom command. The number of columns is the number of specifed values (1 or more). These values can be accessed by any command that uses global array values from a -compute as input. Again, see Section_howto 15 for an overview of LAMMPS output +compute as input. Again, see Section 6.15 for an overview of LAMMPS output options.
The scalar value calculated by this compute is “intensive”. The vector values are “extensive”. The array values are “intensive”.
diff --git a/doc/html/compute_temp_cs.html b/doc/html/compute_temp_cs.html index cfa909d7f1..7fcace42c1 100644 --- a/doc/html/compute_temp_cs.html +++ b/doc/html/compute_temp_cs.html @@ -196,7 +196,7 @@ core/shell pairs, instead of on the individual core and shell atoms. Thermostatting fixes that work in this way include fix nvt, fix temp/rescale, fix temp/berendsen, and fix langevin.The internal energy of core/shell pairs can be calculated by the compute temp/chunk command, if chunks are -defined as core/shell pairs. See Section_howto 25 for more discussion on how to do this.
+defined as core/shell pairs. See Section 6.25 for more discussion on how to do this.Output info:
This compute calculates a global scalar (the temperature) and a global
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
diff --git a/doc/html/compute_ti.html b/doc/html/compute_ti.html
index 8d6198637d..c55e4a6643 100644
--- a/doc/html/compute_ti.html
+++ b/doc/html/compute_ti.html
@@ -223,7 +223,7 @@ du/dl can be found in the paper by Output info:
This compute calculates a global scalar, namely dUs/dlambda. This value can be used by any command that uses a global scalar value from -a compute as input. See Section_howto 15 for an overview of LAMMPS output +a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The scalar value calculated by this compute is “extensive”.
The scalar value will be in energy units.
diff --git a/doc/html/compute_torque_chunk.html b/doc/html/compute_torque_chunk.html index 650ce622aa..2c086faf09 100644 --- a/doc/html/compute_torque_chunk.html +++ b/doc/html/compute_torque_chunk.html @@ -150,7 +150,7 @@ atoms.In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for 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 3 components of the torque vector for eqch diff --git a/doc/html/compute_vcm_chunk.html b/doc/html/compute_vcm_chunk.html index c8574fa37f..da7a8f04a7 100644 --- a/doc/html/compute_vcm_chunk.html +++ b/doc/html/compute_vcm_chunk.html @@ -150,7 +150,7 @@ multiple chunks of atoms.
In LAMMPS, chunks are collections of atoms defined by a compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for 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 components of the center-of-mass @@ -177,7 +177,7 @@ fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector number of chunks Nchunk as calculated by the specified compute chunk/atom command. The number of columns = 3 for the x,y,z center-of-mass velocity coordinates of each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +values from a compute as input. See Section 6.15 for an overview of LAMMPS output options.
The array values are “intensive”. The array values will be in velocity units.
diff --git a/doc/html/compute_voronoi_atom.html b/doc/html/compute_voronoi_atom.html index ed4cd612a1..a9c8622ebf 100644 --- a/doc/html/compute_voronoi_atom.html +++ b/doc/html/compute_voronoi_atom.html @@ -296,7 +296,7 @@ columns. In regular dynamic tessellation mode the first column is the Voronoi volume, the second is the neighbor count, as described above (read above for the output data in case the occupation keyword is specified). These values can be accessed by any command that uses -per-atom values from a compute as input. See Section_howto 15 for an overview of LAMMPS output +per-atom values from a compute as input. See Section 6.15 for an overview of LAMMPS output options. If the peratom keyword is set to “no”, the per-atom array is still created, but it is not accessible.If the edge_histo keyword is used, then this compute generates a diff --git a/doc/html/fix_ave_chunk.html b/doc/html/fix_ave_chunk.html index a6293fb62e..53e07808c9 100644 --- a/doc/html/fix_ave_chunk.html +++ b/doc/html/fix_ave_chunk.html @@ -214,7 +214,7 @@ averages can be used by other compute chunk/atom command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a -molecule or atoms in a spatial bin. See the compute chunk/atom doc page and “Section_howto 23 for details of how chunks can be +molecule or atoms in a spatial bin. See the compute chunk/atom doc page and Section 6.23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system.
Note that only atoms in the specified group contribute to the summing diff --git a/doc/html/fix_nve_body.html b/doc/html/fix_nve_body.html index 45816df757..6b6c04ad8b 100644 --- a/doc/html/fix_nve_body.html +++ b/doc/html/fix_nve_body.html @@ -147,7 +147,7 @@
Perform constant NVE integration to update position, velocity, orientation, and angular velocity for body particles in the group each timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. See Section_howto 14 of the manual and the body +consistent with the microcanonical ensemble. See Section 6.14 of the manual and the body doc page for more details on using body particles.
This fix differs from the fix nve command, which assumes point particles and only updates their position and velocity.
diff --git a/doc/html/fix_nve_manifold_rattle.html b/doc/html/fix_nve_manifold_rattle.html index de2190636f..149e6de046 100644 --- a/doc/html/fix_nve_manifold_rattle.html +++ b/doc/html/fix_nve_manifold_rattle.html @@ -159,7 +159,7 @@ keyword = every atoms constrained to a curved surface (manifold) in the group each timestep. The constraint is handled by RATTLE (Andersen) written out for the special case of single-particle constraints as -explained in (Paquay). V is volume; E is energy. This way, +explained in (Paquay). V is volume; E is energy. This way, the dynamics of particles constrained to curved surfaces can be studied. If combined with fix langevin, this generates Brownian motion of particles constrained to a curved diff --git a/doc/html/fix_viscosity.html b/doc/html/fix_viscosity.html index 16fa977a8f..d3ec7d2bbc 100644 --- a/doc/html/fix_viscosity.html +++ b/doc/html/fix_viscosity.html @@ -221,7 +221,7 @@ accurately infer a viscosity and should try increasing the Nevery parameter.An alternative method for calculating a viscosity is to run a NEMD -simulation, as described in Section_howto 13 of the manual. NEMD simulations +simulation, as described in Section 6.13 of the manual. NEMD simulations deform the simmulation box via the fix deform command. Thus they cannot be run on a charged system using a PPPM solver since PPPM does not currently support non-orthogonal boxes. Using fix viscosity keeps the box orthogonal; diff --git a/doc/html/pair_buck_long.html b/doc/html/pair_buck_long.html index 5d8371e461..edb5973405 100644 --- a/doc/html/pair_buck_long.html +++ b/doc/html/pair_buck_long.html @@ -176,7 +176,7 @@ and Coulombic terms respectively.
The purpose of this pair style is to capture long-range interactions resulting from both attractive 1/r^6 Buckingham and Coulombic 1/r interactions. This is done by use of the flag_buck and flag_coul -settings. The “Ismail paper has more details on when it is +settings. The Ismail paper has more details on when it is appropriate to include long-range 1/r^6 interactions, using this potential.
If flag_buck is set to long, no cutoff is used on the Buckingham diff --git a/doc/html/tad.html b/doc/html/tad.html index e4bab3f210..db9656cac0 100644 --- a/doc/html/tad.html +++ b/doc/html/tad.html @@ -211,7 +211,7 @@ restricts you to having exactly one processor per replica. For more information, see the documentation for the neb command. In the current LAMMPS implementation of TAD, all the non-NEB TAD operations are performed on the first partition, while the other -partitions remain idle. See Section_howto 5 of the manual for further discussion of +partitions remain idle. See Section 6.5 of the manual for further discussion of multi-replica simulations.
A TAD run has several stages, which are repeated each time an event is performed. The logic for a TAD run is as follows:
diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index 0cda354dde..1475daa945 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -44,8 +44,8 @@ model. See "Section 6.10"_Section_howto.html#howto_10 of the manual and the couple directory of the distribution for more ideas about coupling -LAMMPS to other codes. See "Section_howto -19"_Section_howto.html#howto_19 for a description of the LAMMPS +LAMMPS to other codes. See "Section +6.19"_Section_howto.html#howto_19 for a description of the LAMMPS library interface provided in src/library.cpp and src/library.h, and how to extend it for your needs. As described below, that interface is what is exposed to Python either when calling LAMMPS from Python or diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt index 8a73a0dfe0..d2202679c0 100644 --- a/doc/src/Section_start.txt +++ b/doc/src/Section_start.txt @@ -1147,8 +1147,8 @@ description of the Python wrapper provided with LAMMPS that operates through the LAMMPS library interface. The files src/library.cpp and library.h define the C-style API for -using LAMMPS as a library. See "Section_howto -19"_Section_howto.html#howto_19 of the manual for a description of the +using LAMMPS as a library. See "Section +6.19"_Section_howto.html#howto_19 of the manual for a description of the interface and how to extend it for your needs. :line diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index 74b5f0b152..7e2803abdb 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -98,8 +98,8 @@ output the custom values. All of the above styles define point particles, except the {sphere}, {ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and -{body} styles, which define finite-size particles. See "Section_howto -14"_Section_howto.html#howto_14 for an overview of using finite-size +{body} styles, which define finite-size particles. See "Section +6.14"_Section_howto.html#howto_14 for an overview of using finite-size particle models with LAMMPS. All of the point-particle styles assign mass to particles on a diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt index 97722c935d..439ff5192c 100644 --- a/doc/src/compute_angmom_chunk.txt +++ b/doc/src/compute_angmom_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -73,8 +73,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the angular momentum for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt index af0185e37d..b59a3fd4c8 100644 --- a/doc/src/compute_basal_atom.txt +++ b/doc/src/compute_basal_atom.txt @@ -46,8 +46,8 @@ in examples/USER/misc/basal. This compute calculates a per-atom array with 3 columns, which can be accessed by indices 1-3 by any command that uses per-atom values from -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector values are unitless since the 3 columns represent diff --git a/doc/src/compute_centro_atom.txt b/doc/src/compute_centro_atom.txt index 17403d71e9..2a3ae15aaf 100644 --- a/doc/src/compute_centro_atom.txt +++ b/doc/src/compute_centro_atom.txt @@ -97,8 +97,8 @@ too frequently or to have multiple compute/dump commands, each with a By default, this compute calculates the centrosymmetry 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 "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. If the {axes} keyword setting is {yes}, then a per-atom array is diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index 82d33c0038..2778be4f6b 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -101,8 +101,8 @@ msd/chunk"_compute_msd_chunk.html. Or they can be used by the "fix ave/chunk"_fix_ave_chunk.html command to sum and time average a variety of per-atom properties over the atoms in each chunk. Or they can simply be accessed by any command that uses per-atom values from a -compute as input, as discussed in "Section_howto -15"_Section_howto.html#howto_15. +compute as input, as discussed in "Section +6.15"_Section_howto.html#howto_15. See "Section 6.23"_Section_howto.html#howto_23 for an overview of how this compute can be used with a variety of other commands to diff --git a/doc/src/compute_com_chunk.txt b/doc/src/compute_com_chunk.txt index b7b367e01a..d497585cb0 100644 --- a/doc/src/compute_com_chunk.txt +++ b/doc/src/compute_com_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -71,8 +71,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 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 "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_coord_atom.txt b/doc/src/compute_coord_atom.txt index 123feaf7dc..012a87a9a7 100644 --- a/doc/src/compute_coord_atom.txt +++ b/doc/src/compute_coord_atom.txt @@ -76,8 +76,8 @@ If single {type1} keyword is specified (or if none are specified), this compute calculates a per-atom vector. If multiple {typeN} keywords are specified, this compute calculates a per-atom array, with N columns. These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom vector or array values will be a number >= 0.0, as diff --git a/doc/src/compute_dipole_chunk.txt b/doc/src/compute_dipole_chunk.txt index 0d2a8011e2..7dfddfd6a1 100644 --- a/doc/src/compute_dipole_chunk.txt +++ b/doc/src/compute_dipole_chunk.txt @@ -32,8 +32,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -76,8 +76,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 4 for the 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 "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +array values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 7420dffef0..566dcfc0a0 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -53,8 +53,8 @@ correctly with time=0 atom coordinates from the restart file. 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 -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom array values will be in distance "units"_units.html. diff --git a/doc/src/compute_dpd_atom.txt b/doc/src/compute_dpd_atom.txt index 0ce40f66f4..f586e0f092 100644 --- a/doc/src/compute_dpd_atom.txt +++ b/doc/src/compute_dpd_atom.txt @@ -36,7 +36,7 @@ particles. This compute calculates a per-particle array with 4 columns (u_cond, u_mech, u_chem, dpdTheta), which can be accessed by indices 1-4 by any command that uses per-particle values from a compute as input. See -"Section_howto15"_Section_howto.html#howto_15 for an overview of +"Section 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-particle array values will be in energy (u_cond, u_mech, u_chem) diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt index c5fb2f0b70..f4325f620f 100644 --- a/doc/src/compute_fep.txt +++ b/doc/src/compute_fep.txt @@ -219,8 +219,8 @@ unperturbed parameters. The energies include kspace terms if these are used in the simulation. These output results can be used by any command that uses a global -scalar or vector from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +scalar or vector from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. For example, the computed values can be averaged using "fix ave/time"_fix_ave_time.html. diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt index dc03234dee..dd71431527 100644 --- a/doc/src/compute_gyration.txt +++ b/doc/src/compute_gyration.txt @@ -55,8 +55,8 @@ using the "set image"_set.html command. This compute calculates a global scalar (Rg) and a global vector of length 6 (Rg^2 tensor), which can be accessed by indices 1-6. These values can be used by any command that uses a global scalar value or -vector values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +vector values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar and vector values calculated by this compute are diff --git a/doc/src/compute_gyration_chunk.txt b/doc/src/compute_gyration_chunk.txt index 53b35213b0..3beecce58f 100644 --- a/doc/src/compute_gyration_chunk.txt +++ b/doc/src/compute_gyration_chunk.txt @@ -35,8 +35,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. diff --git a/doc/src/compute_hexorder_atom.txt b/doc/src/compute_hexorder_atom.txt index bbcab832b0..c6f111a6cc 100644 --- a/doc/src/compute_hexorder_atom.txt +++ b/doc/src/compute_hexorder_atom.txt @@ -96,8 +96,8 @@ real and imaginary parts {qn}, a complex number restricted to the unit disk of the complex plane i.e. Re({qn})^2 + Im({qn})^2 <= 1 . These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt index 6f28ed0aa5..215f3c1a8a 100644 --- a/doc/src/compute_inertia_chunk.txt +++ b/doc/src/compute_inertia_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -72,8 +72,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 6 for the 6 components of the inertia tensor for each chunk, ordered as listed above. These values can be accessed by any command that -uses global array values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +uses global array values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_ke_rigid.txt b/doc/src/compute_ke_rigid.txt index 4e65cae72e..f79696a77a 100644 --- a/doc/src/compute_ke_rigid.txt +++ b/doc/src/compute_ke_rigid.txt @@ -40,8 +40,8 @@ calculation. This compute calculates a global scalar (the summed KE 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 "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +global scalar value from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt index 8d3ba07857..7382ca87de 100644 --- a/doc/src/compute_msd_chunk.txt +++ b/doc/src/compute_msd_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. diff --git a/doc/src/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt index 8c09cecfce..46c72d3dcb 100644 --- a/doc/src/compute_omega_chunk.txt +++ b/doc/src/compute_omega_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -73,8 +73,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the 3 xyz components of the angular velocity for each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_orientorder_atom.txt b/doc/src/compute_orientorder_atom.txt index 11579fe627..3b6c58c826 100644 --- a/doc/src/compute_orientorder_atom.txt +++ b/doc/src/compute_orientorder_atom.txt @@ -99,8 +99,8 @@ This compute calculates a per-atom array with {nlvalues} columns, giving the {Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1. These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. [Restrictions:] none diff --git a/doc/src/compute_pe.txt b/doc/src/compute_pe.txt index 2e3f5d8beb..15f27a8eff 100644 --- a/doc/src/compute_pe.txt +++ b/doc/src/compute_pe.txt @@ -64,8 +64,8 @@ See the "thermo_style" command for more details. This compute calculates a global scalar (the potential energy). This value can be used by any command that uses a global scalar value from -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". The diff --git a/doc/src/compute_property_chunk.txt b/doc/src/compute_property_chunk.txt index c10fe56455..578a6df343 100644 --- a/doc/src/compute_property_chunk.txt +++ b/doc/src/compute_property_chunk.txt @@ -36,8 +36,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. diff --git a/doc/src/compute_smd_ulsph_strain_rate.txt b/doc/src/compute_smd_ulsph_strain_rate.txt index 3f32e43912..eb9318e072 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.txt +++ b/doc/src/compute_smd_ulsph_strain_rate.txt @@ -32,8 +32,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The values will be given in "units"_units.html of one over time. diff --git a/doc/src/compute_smd_ulsph_stress.txt b/doc/src/compute_smd_ulsph_stress.txt index 4d1994e37c..115a4d14bb 100644 --- a/doc/src/compute_smd_ulsph_stress.txt +++ b/doc/src/compute_smd_ulsph_stress.txt @@ -30,8 +30,8 @@ Mach Dynamics in LAMMPS. This compute calculates a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values -from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The values will be given in "units"_units.html of pressure. diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index b8e3f9b732..7f10fdbcce 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -205,8 +205,8 @@ notation. Each of these sub-blocks contains one column for each bispectrum component, the same as for compute {sna/atom} These values can be accessed by any command that uses per-atom values -from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. [Restrictions:] diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index 35e586068b..2749478439 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -137,8 +137,8 @@ thermo_style custom step temp etotal press v_press :pre This compute calculates a per-atom array with 6 columns, which can be accessed by indices 1-6 by any command that uses per-atom values from -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The per-atom array values will be in pressure*volume diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index 826d0f6e00..d565c95134 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -52,8 +52,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -210,8 +210,8 @@ of the optional values are specified. The number of rows in the array "compute chunk/atom"_compute_chunk_atom.html command. The number of columns is the number of specifed values (1 or more). These values can be accessed by any command that uses global array values from a -compute as input. Again, see "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +compute as input. Again, see "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "intensive". The diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt index 7170ef951e..46846d6ee5 100644 --- a/doc/src/compute_temp_cs.txt +++ b/doc/src/compute_temp_cs.txt @@ -83,8 +83,8 @@ langevin"_fix_langevin.html. The internal energy of core/shell pairs can be calculated by the "compute temp/chunk"_compute_temp_chunk.html command, if chunks are -defined as core/shell pairs. See "Section_howto -25"_Section_howto.html#howto_25 for more discussion on how to do this. +defined as core/shell pairs. See "Section +6.25"_Section_howto.html#howto_25 for more discussion on how to do this. [Output info:] diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt index 1fbbb592f2..71b62281dc 100644 --- a/doc/src/compute_ti.txt +++ b/doc/src/compute_ti.txt @@ -111,8 +111,8 @@ du/dl can be found in the paper by "Eike"_#Eike. This compute calculates a global scalar, namely dUs/dlambda. This value can be used by any command that uses a global scalar value from -a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The scalar value calculated by this compute is "extensive". diff --git a/doc/src/compute_torque_chunk.txt b/doc/src/compute_torque_chunk.txt index 334152b041..b9f832dd03 100644 --- a/doc/src/compute_torque_chunk.txt +++ b/doc/src/compute_torque_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. diff --git a/doc/src/compute_vcm_chunk.txt b/doc/src/compute_vcm_chunk.txt index 0b9154713f..de02c586bf 100644 --- a/doc/src/compute_vcm_chunk.txt +++ b/doc/src/compute_vcm_chunk.txt @@ -30,8 +30,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. @@ -63,8 +63,8 @@ number of chunks {Nchunk} as calculated by the specified "compute chunk/atom"_compute_chunk_atom.html command. The number of columns = 3 for the x,y,z center-of-mass velocity coordinates of each chunk. These values can be accessed by any command that uses global array -values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The array values are "intensive". The array values will be in diff --git a/doc/src/compute_voronoi_atom.txt b/doc/src/compute_voronoi_atom.txt index 3dcdffacb1..899fc84388 100644 --- a/doc/src/compute_voronoi_atom.txt +++ b/doc/src/compute_voronoi_atom.txt @@ -186,8 +186,8 @@ columns. In regular dynamic tessellation mode the first column is the Voronoi volume, the second is the neighbor count, as described above (read above for the output data in case the {occupation} keyword is specified). These values can be accessed by any command that uses -per-atom values from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output +per-atom values from a compute as input. See "Section +6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output options. If the {peratom} keyword is set to "no", the per-atom array is still created, but it is not accessible. diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index d02fa17e10..3ed91c8612 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -94,8 +94,8 @@ chunk/atom"_compute_chunk_atom.html command, which assigns each atom to a single chunk (or no chunk). The ID for this command is specified as chunkID. For example, a single chunk could be the atoms in a molecule or atoms in a spatial bin. See the "compute -chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto -23"_Section_howto.html#howto_23 for details of how chunks can be +chunk/atom"_compute_chunk_atom.html doc page and "Section +6.23"_Section_howto.html#howto_23 for details of how chunks can be defined and examples of how they can be used to measure properties of a system. diff --git a/doc/src/fix_nve_body.txt b/doc/src/fix_nve_body.txt index 77d0a5e909..0f80d3aa7a 100755 --- a/doc/src/fix_nve_body.txt +++ b/doc/src/fix_nve_body.txt @@ -24,8 +24,8 @@ fix 1 all nve/body :pre Perform constant NVE integration to update position, velocity, orientation, and angular velocity for body particles in the group each timestep. V is volume; E is energy. This creates a system trajectory -consistent with the microcanonical ensemble. See "Section_howto -14"_Section_howto.html#howto_14 of the manual and the "body"_body.html +consistent with the microcanonical ensemble. See "Section +6.14"_Section_howto.html#howto_14 of the manual and the "body"_body.html doc page for more details on using body particles. This fix differs from the "fix nve"_fix_nve.html command, which diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index 744197256d..a5e8b41560 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -100,8 +100,8 @@ accurately infer a viscosity and should try increasing the Nevery parameter. An alternative method for calculating a viscosity is to run a NEMD -simulation, as described in "Section_howto -13"_Section_howto.html#howto_13 of the manual. NEMD simulations +simulation, as described in "Section +6.13"_Section_howto.html#howto_13 of the manual. NEMD simulations deform the simmulation box via the "fix deform"_fix_deform.html command. Thus they cannot be run on a charged system using a "PPPM solver"_kspace_style.html since PPPM does not currently support diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt index 752ef71f98..ba18738e4d 100644 --- a/doc/src/pair_buck_long.txt +++ b/doc/src/pair_buck_long.txt @@ -48,7 +48,7 @@ and Coulombic terms respectively. The purpose of this pair style is to capture long-range interactions resulting from both attractive 1/r^6 Buckingham and Coulombic 1/r interactions. This is done by use of the {flag_buck} and {flag_coul} -settings. The ""Ismail"_#Ismail paper has more details on when it is +settings. The "Ismail"_#Ismail paper has more details on when it is appropriate to include long-range 1/r^6 interactions, using this potential. diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 8e93b93c3b..8a0bd31c74 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -92,8 +92,8 @@ restricts you to having exactly one processor per replica. For more information, see the documentation for the "neb"_neb.html command. In the current LAMMPS implementation of TAD, all the non-NEB TAD operations are performed on the first partition, while the other -partitions remain idle. See "Section_howto -5"_Section_howto.html#howto_5 of the manual for further discussion of +partitions remain idle. See "Section +6.5"_Section_howto.html#howto_5 of the manual for further discussion of multi-replica simulations. A TAD run has several stages, which are repeated each time an event is