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make links unique, fix doc format warnings and add entries to administrative files

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This commit is contained in:
Axel Kohlmeyer
2017-08-23 00:39:52 -04:00
parent b80752a40c
commit cdfb1aa043
11 changed files with 32 additions and 25 deletions
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5
doc/src/compute_edpd_temp_atom.txt
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@ -26,7 +26,8 @@ for each eDPD particle in a group.
The temperature is a local temperature derived from the internal energy
of each eDPD particle based on the local equilibrium hypothesis.
For more details please see "(Espanol1997)"_#Espanol1997 and "(Li2014)"_#Li2014.
For more details please see "(Espanol1997)"_#Espanol1997 and
"(Li2014)"_#Li2014a.
[Output info:]
@ -55,7 +56,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
[(Espanol1997)] Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI:
10.1209/epl/i1997-00515-8
:link(Li2014)
:link(Li2014a)
[(Li2014)] Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265:
113-127 (2014). DOI: 10.1016/j.jcp.2014.02.003.

4
doc/src/compute_tdpd_cc_atom.txt
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@ -28,7 +28,7 @@ group.
The chemical concentration of each species is defined as the number of
molecules carried by a tDPD particle for dilute solution. For more
details see "(Li2015)"_#Li2015.
details see "(Li2015)"_#Li2015a.
[Output info:]
@ -54,7 +54,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
:line
:link(Li2015)
:link(Li2015a)
[(Li2015)] Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143:
014101 (2015). DOI: 10.1063/1.4923254

2
doc/src/computes.txt
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@ -30,6 +30,7 @@ Computes :h1
compute_displace_atom
compute_dpd
compute_dpd_atom
compute_edpd_temp_atom
compute_erotate_asphere
compute_erotate_rigid
compute_erotate_sphere
@ -95,6 +96,7 @@ Computes :h1
compute_sna_atom
compute_stress_atom
compute_tally
compute_tdpd_cc_atom
compute_temp
compute_temp_asphere
compute_temp_body

8
doc/src/fix_dpd_source.txt
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@ -46,8 +46,8 @@ where the {source} is in units of mole/volume/time.
This command can be used to give an additional heat/concentration
source term to atoms in a simulation, such as for a simulation of a
heat conduction with a source term (see Fig.12 in "(Li2014)"_#Li2014)
or diffusion with a source term (see Fig.1 in "(Li2015)"_#Li2015), as
heat conduction with a source term (see Fig.12 in "(Li2014)"_#Li2014b)
or diffusion with a source term (see Fig.1 in "(Li2015)"_#Li2015b), as
an analog of a periodic Poiseuille flow problem.
If the {sphere} keyword is used, the {cx,cy,cz,radius} defines a
@ -88,13 +88,13 @@ tdpd/cc/atom"_compute_tdpd_cc_atom.html
:line
:link(Li2014)
:link(Li2014b)
[(Li2014)] Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis,
"Energy-conserving dissipative particle dynamics with
temperature-dependent properties", J. Comput. Phys., 265: 113-127
(2014). DOI: 10.1016/j.jcp.2014.02.003
:link(Li2015)
:link(Li2015b)
[(Li2015)] Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis,
"Transport dissipative particle dynamics model for mesoscopic
advection-diffusion-reaction problems", J. Chem. Phys., 143: 014101

4
doc/src/fix_mvv_dpd.txt
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@ -48,7 +48,7 @@ case-by-case basis. Specification of a {lambda} value is opttional.
If specified, the setting must be from 0.0 to 1.0. If not specified,
a default value of 0.5 is used, which effectively reproduces the
standard velocity-Verlet (VV) scheme. For more details, see
"Groot"_#Groot.
"Groot"_#Groot2.
Fix {mvv/dpd} updates the position and velocity of each atom. It can
be used with the "pair_style mdpd"_pair_meso.html command or other
@ -91,7 +91,7 @@ The default value for the optional {lambda} parameter is 0.5.
:line
:link(Groot)
:link(Groot2)
[(Groot)] Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI:
10.1063/1.474784

2
doc/src/fixes.txt
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@ -33,6 +33,7 @@ Fixes :h1
fix_drude
fix_drude_transform
fix_dpd_energy
fix_dpd_source
fix_dt_reset
fix_efield
fix_ehex
@ -71,6 +72,7 @@ Fixes :h1
fix_move
fix_mscg
fix_msst
fix_mvv_dpd
fix_neb
fix_nh
fix_nh_eff

6
doc/src/lammps.book
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@ -156,6 +156,7 @@ fix_controller.html
fix_deform.html
fix_deposit.html
fix_dpd_energy.html
fix_dpd_source.html
fix_drag.html
fix_drude.html
fix_drude_transform.html
@ -197,6 +198,7 @@ fix_momentum.html
fix_move.html
fix_mscg.html
fix_msst.html
fix_mvv_dpd.html
fix_neb.html
fix_nh.html
fix_nh_eff.html
@ -315,6 +317,7 @@ compute_dipole_chunk.html
compute_displace_atom.html
compute_dpd.html
compute_dpd_atom.html
compute_edpd_temp_atom.html
compute_erotate_asphere.html
compute_erotate_rigid.html
compute_erotate_sphere.html
@ -380,6 +383,7 @@ compute_smd_vol.html
compute_sna_atom.html
compute_stress_atom.html
compute_tally.html
compute_tdpd_cc_atom.html
compute_temp.html
compute_temp_asphere.html
compute_temp_body.html
@ -457,6 +461,7 @@ pair_mdf.html
pair_meam.html
pair_meam_spline.html
pair_meam_sw_spline.html
pair_meso.html
pair_mgpt.html
pair_mie.html
pair_momb.html
@ -644,4 +649,3 @@ USER/atc/man_unfix_flux.html
USER/atc/man_unfix_nodes.html
USER/atc/man_write_atom_weights.html
USER/atc/man_write_restart.html

4
doc/src/pair_dpd.txt
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@ -36,7 +36,7 @@ pair_coeff 1 1 1.0 1.0 :pre
[Description:]
Style {dpd} computes a force field for dissipative particle dynamics
(DPD) following the exposition in "(Groot)"_#Groot.
(DPD) following the exposition in "(Groot)"_#Groot1.
Style {dpd/tstat} invokes a DPD thermostat on pairwise interactions,
which is equivalent to the non-conservative portion of the DPD force
@ -196,7 +196,7 @@ langevin"_fix_langevin.html, "pair_style srp"_pair_srp.html
:line
:link(Groot)
:link(Groot1)
[(Groot)] Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
:link(Afshar)

14
doc/src/pair_snap.txt
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@ -10,8 +10,7 @@ pair_style snap command :h3
[Syntax:]
pair_style snap
:pre
pair_style snap :pre
[Examples:]
@ -20,17 +19,16 @@ pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre
[Description:]
Pair style {snap} computes interactions
using the spectral neighbor analysis potential (SNAP)
"(Thompson)"_#Thompson20142. Like the GAP framework of Bartok et al.
"(Bartok2010)"_#Bartok20102, "(Bartok2013)"_#Bartok2013
which uses bispectrum components
Pair style {snap} computes interactions using the spectral
neighbor analysis potential (SNAP) "(Thompson)"_#Thompson20142.
Like the GAP framework of Bartok et al. "(Bartok2010)"_#Bartok20102,
"(Bartok2013)"_#Bartok2013 which uses bispectrum components
to characterize the local neighborhood of each atom
in a very general way. The mathematical definition of the
bispectrum calculation used by SNAP is identical
to that used by "compute sna/atom"_compute_sna_atom.html.
In SNAP, the total energy is decomposed into a sum over
atom energies. The energy of atom {i } is
atom energies. The energy of atom {i} is
expressed as a weighted sum over bispectrum components.
:c,image(Eqs/pair_snap.jpg)

1
doc/src/pairs.txt
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@ -58,6 +58,7 @@ Pair Styles :h1
pair_meam
pair_meam_spline
pair_meam_sw_spline
pair_meso
pair_mgpt
pair_mie
pair_momb

7
doc/src/read_data.txt
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@ -374,10 +374,9 @@ needed if new bonds (angles, dihedrals, impropers) will be added to
the system when a simulation runs, e.g. by using the "fix
bond/create"_fix_bond_create.html command. Using this header flag
is deprecated; please use the {extra/bond/per/atom} keyword (and
correspondingly for angles, dihedrals and impropers) in the
read_data command instead. Either will pre-allocate space in LAMMPS
data structures for storing the new bonds (angles,
dihedrals, impropers).
correspondingly for angles, dihedrals and impropers) in the read_data
command instead. Either will pre-allocate space in LAMMPS data
structures for storing the new bonds (angles, dihedrals, impropers).
The "extra special per atom" setting is typically only needed if new
bonds/angles/etc will be added to the system, e.g. by using the "fix