ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

fix a bunch of broken linke or make links unique across files

Browse Source
This commit is contained in:
Axel Kohlmeyer
2018-08-09 16:50:09 +02:00
parent a97ad15d22
commit df20fbbca4
11 changed files with 23 additions and 19 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
doc/src/Commands_bond.txt
View File

@ -9,7 +9,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
"Bond styles"_Commands_bond.html,
"Bond styles"_Commands_bond.html#bond,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,

4
doc/src/Howto_tip4p.txt
View File

@ -31,7 +31,7 @@ using the "fix shake"_fix_shake.html command.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in
"(Jorgensen)"_#Jorgensen5. Note that the OM distance is specified in
the "pair_style"_pair_style.html command, not as part of the pair
coefficients.
@ -107,6 +107,6 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
:link(Jorgensen1)
:link(Jorgensen5)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).

4
doc/src/Intro_features.txt
View File

@ -20,7 +20,7 @@ classes of functionality:
"Integrators"_#integrate
"Diagnostics"_#diag
"Output"_#output
"Multi-replica models"_#replica
"Multi-replica models"_#replica1
"Pre- and post-processing"_#prepost
"Specialized features (beyond MD itself)"_#special :ul
@ -154,7 +154,7 @@ Output :h4,link(output)
time averaging of system-wide quantities
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
Multi-replica models :h4,link(replica)
Multi-replica models :h4,link(replica1)
"nudged elastic band"_neb.html
"parallel replica dynamics"_prd.html

6
doc/src/Manual.txt
View File

@ -8,6 +8,8 @@
<BODY>
<H1></H1>
<!-- END_HTML_ONLY -->
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
@ -18,8 +20,6 @@
:line
<H1></H1>
LAMMPS Documentation :c,h1
2 Aug 2018 version :c,h2
@ -71,6 +71,7 @@ every LAMMPS command.
:name: userdoc
:includehidden:
Manual_version
Intro
Section_start
Commands
@ -82,6 +83,7 @@ every LAMMPS command.
Modify
Python
Errors
Build_manual
.. toctree::
:caption: Index

8
doc/src/Packages_details.txt
View File

@ -49,7 +49,7 @@ as contained in the file name.
"PYTHON"_#PYTHON,
"QEQ"_#QEQ,
"REAX"_#REAX,
"REPLICA"_#REPLICA,
"REPLICA"_#REPLICA2,
"RIGID"_#RIGID,
"SHOCK"_#SHOCK,
"SNAP"_#SNAP,
@ -392,7 +392,7 @@ src/GPU: filenames -> commands
src/GPU/README
lib/gpu/README
"Speed packages"_Speed_packages.html
"Speed gpu"_Speed_gpu.html.html
"Speed gpu"_Speed_gpu.html
"Section 2.6 -sf gpu"_Section_start.html#start_6
"Section 2.6 -pk gpu"_Section_start.html#start_6
"package gpu"_package.html
@ -1225,7 +1225,7 @@ examples/reax :ul
:line
REPLICA package :link(REPLICA),h4
REPLICA package :link(REPLICA2),h4
[Contents:]
@ -1373,7 +1373,7 @@ make machine :pre
[Supporting info:]
src/SPIN: filenames -> commands
"Howto spin"_Howto_spin.html
"Howto spins"_Howto_spins.html
"pair_style spin/dmi"_pair_spin_dmi.html
"pair_style spin/exchange"_pair_spin_exchange.html
"pair_style spin/magelec"_pair_spin_magelec.html

4
doc/src/Packages_standard.txt
View File

@ -57,9 +57,9 @@ Package, Description, Doc page, Example, Library
"PYTHON"_Packages_details.html#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_Packages_details.html#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
"REAX"_Packages_details.html#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
"REPLICA"_Packages_details.html#REPLICA, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
"REPLICA"_Packages_details.html#REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
"RIGID"_Packages_details.html#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_Packages_details.html#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
"SNAP"_Packages_details.html#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spin"_Howto_spin.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"VORONOI"_Packages_details.html#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)

2
doc/src/Python_install.txt
View File

@ -68,7 +68,7 @@ need to prefix this with "sudo". In this mode you cannot control
which Python is invoked by root.
Note that if you want Python to be able to load different versions of
the LAMMPS shared library (see "this section"_#py_5 below), you will
the LAMMPS shared library (see "this section"_Python_shlib.html), you will
need to manually copy files like liblammps_g++.so into the appropriate
system directory. This is not needed if you set the LD_LIBRARY_PATH
environment variable as described above.

3
doc/src/Python_shlib.txt
View File

@ -31,4 +31,5 @@ extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
"Section 2.4"_Section_start.html#start_4 for more details.
Also include CMake info on this
TODO: Also include CMake info on this

2
doc/src/fix_manifoldforce.txt
View File

@ -24,7 +24,7 @@ fix constrain all manifoldforce sphere 5.0
[Description:]
This fix subtracts each time step from the force the component along the normal of the specified "manifold"_manifolds.html.
This fix subtracts each time step from the force the component along the normal of the specified "manifold"_Howto_manifold.html.
This can be used in combination with "minimize"_minimize.html to remove overlap between particles while
keeping them (roughly) constrained to the given manifold, e.g. to set up a run with "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html.
I have found that only {hftn} and {quickmin} with a very small time step perform adequately though.

3
doc/src/fix_property_atom.txt
View File

@ -200,7 +200,8 @@ added classes.
:line
:link(isotopes) Example for using per-atom masses with TIP4P water to
:link(isotopes)
Example for using per-atom masses with TIP4P water to
study isotope effects. When setting up simulations with the "TIP4P
pair styles"_Howto_tip4p.html for water, you have to provide exactly
one atom type each to identify the water oxygen and hydrogen

4
doc/src/fix_wall_reflect.txt
View File

@ -51,7 +51,7 @@ corresponding component of its velocity is flipped.
When used in conjunction with "fix nve"_fix_nve.html and "run_style
verlet"_run_style.html, the resultant time-integration algorithm is
equivalent to the primitive splitting algorithm (PSA) described by
"Bond"_#Bond. Because each reflection event divides
"Bond"_#Bond1. Because each reflection event divides
the corresponding timestep asymmetrically, energy conservation is only
satisfied to O(dt), rather than to O(dt^2) as it would be for
velocity-Verlet integration without reflective walls.
@ -179,5 +179,5 @@ error.
:line
:link(Bond)
:link(Bond1)
[(Bond)] Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).