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Merge pull request #744 from akohlmey/doc-update

Browse Source 
Documentation build updates
This commit is contained in:
Steve Plimpton
2018-01-08 09:15:02 -07:00
committed by GitHub
parent 8888b05b18 3291a4fe96
commit 1b51efd6b8
13 changed files with 62 additions and 55 deletions
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7
doc/Makefile
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@ -20,6 +20,7 @@ ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
HAS_VIRTUALENV = YES HAS_VIRTUALENV = YES
endif endif
SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
SOURCES=$(wildcard src/*.txt) SOURCES=$(wildcard src/*.txt)
OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst) OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
@ -55,7 +56,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
@(\ @(\
. $(VENV)/bin/activate ;\ . $(VENV)/bin/activate ;\
cp -r src/* $(RSTDIR)/ ;\ cp -r src/* $(RSTDIR)/ ;\
sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\ sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
echo "############################################" ;\ echo "############################################" ;\
doc_anchor_check src/*.txt ;\ doc_anchor_check src/*.txt ;\
echo "############################################" ;\ echo "############################################" ;\
@ -91,7 +92,7 @@ epub: $(OBJECTS)
@(\ @(\
. $(VENV)/bin/activate ;\ . $(VENV)/bin/activate ;\
cp -r src/* $(RSTDIR)/ ;\ cp -r src/* $(RSTDIR)/ ;\
sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\ sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
deactivate ;\ deactivate ;\
) )
@mv epub/LAMMPS.epub . @mv epub/LAMMPS.epub .
@ -159,7 +160,7 @@ $(VENV):
@( \ @( \
virtualenv -p $(PYTHON) $(VENV); \ virtualenv -p $(PYTHON) $(VENV); \
. $(VENV)/bin/activate; \ . $(VENV)/bin/activate; \
pip install Sphinx==1.5.6; \ pip install Sphinx; \
pip install sphinxcontrib-images; \ pip install sphinxcontrib-images; \
deactivate;\ deactivate;\
) )

2
doc/src/Section_howto.txt
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@ -454,7 +454,7 @@ NOTE: By default, for 2d systems, granular particles are still modeled
as 3d spheres, not 2d discs (circles), meaning their moment of inertia as 3d spheres, not 2d discs (circles), meaning their moment of inertia
will be the same as in 3d. If you wish to model granular particles in will be the same as in 3d. If you wish to model granular particles in
2d as 2d discs, see the note on this topic in "Section 2d as 2d discs, see the note on this topic in "Section
6.2"_Section_howto.html#howto_2, where 2d simulations are disussed. 6.2"_Section_howto.html#howto_2, where 2d simulations are discussed.
:line :line

16
doc/src/Section_packages.txt
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@ -243,7 +243,7 @@ COLLOID package :link(COLLOID),h4
[Contents:] [Contents:]
Coarse-grained finite-size colloidal particles. Pair stayle and fix Coarse-grained finite-size colloidal particles. Pair styles and fix
wall styles for colloidal interactions. Includes the Fast Lubrication wall styles for colloidal interactions. Includes the Fast Lubrication
Dynamics (FLD) method for hydrodynamic interactions, which is a Dynamics (FLD) method for hydrodynamic interactions, which is a
simplified approximation to Stokesian dynamics. simplified approximation to Stokesian dynamics.
@ -734,7 +734,7 @@ make lib-latte args="-b -m gfortran" # download and build in lib/latte and
Note that 3 symbolic (soft) links, "includelink" and "liblink" and Note that 3 symbolic (soft) links, "includelink" and "liblink" and
"filelink", are created in lib/latte to point into the LATTE home dir. "filelink", are created in lib/latte to point into the LATTE home dir.
When LAMMPS builds in src it will use these links. You should When LAMMPS builds in src it will use these links. You should
also check that the Makefile.lammps file you create is apporpriate also check that the Makefile.lammps file you create is appropriate
for the compiler you use on your system to build LATTE. for the compiler you use on your system to build LATTE.
You can then install/un-install the package and build LAMMPS in the You can then install/un-install the package and build LAMMPS in the
@ -984,7 +984,7 @@ MSCG package :link(mscg),h4
[Contents:] [Contents:]
A "fix mscg"_fix_mscg.html command which can parameterize a A "fix mscg"_fix_mscg.html command which can parameterize a
Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
library"_mscg_home. library"_mscg_home.
:link(mscg_home,https://github.com/uchicago-voth/MSCG-release) :link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
@ -1781,7 +1781,7 @@ coarse-grained DPD-based models for energetic, reactive molecular
crystalline materials. It includes many pair styles specific to these crystalline materials. It includes many pair styles specific to these
systems, including for reactive DPD, where each particle has internal systems, including for reactive DPD, where each particle has internal
state for multiple species and a coupled set of chemical reaction ODEs state for multiple species and a coupled set of chemical reaction ODEs
are integrated each timestep. Highly accurate time intergrators for are integrated each timestep. Highly accurate time integrators for
isothermal, isoenergetic, isobaric and isenthalpic conditions are isothermal, isoenergetic, isobaric and isenthalpic conditions are
included. These enable long timesteps via the Shardlow splitting included. These enable long timesteps via the Shardlow splitting
algorithm. algorithm.
@ -2231,7 +2231,7 @@ Several extensions of the the dissipative particle dynamics (DPD)
method. Specifically, energy-conserving DPD (eDPD) that can model method. Specifically, energy-conserving DPD (eDPD) that can model
non-isothermal processes, many-body DPD (mDPD) for simulating non-isothermal processes, many-body DPD (mDPD) for simulating
vapor-liquid coexistence, and transport DPD (tDPD) for modeling vapor-liquid coexistence, and transport DPD (tDPD) for modeling
advection-diffuion-reaction systems. The equations of motion of these advection-diffusion-reaction systems. The equations of motion of these
DPD extensions are integrated through a modified velocity-Verlet (MVV) DPD extensions are integrated through a modified velocity-Verlet (MVV)
algorithm. algorithm.
@ -2495,7 +2495,7 @@ make machine :pre
NOTE: The LAMMPS executable these steps produce is not yet functional NOTE: The LAMMPS executable these steps produce is not yet functional
for a QM/MM simulation. You must also build Quantum ESPRESSO and for a QM/MM simulation. You must also build Quantum ESPRESSO and
create a new executable which links LAMMPS and Quanutm ESPRESSO create a new executable which links LAMMPS and Quantum ESPRESSO
together. These are steps 3 and 4 described in the lib/qmmm/README together. These are steps 3 and 4 described in the lib/qmmm/README
file. file.
@ -2554,7 +2554,7 @@ developed by the Cambridge University group.
:link(quip,https://github.com/libAtoms/QUIP) :link(quip,https://github.com/libAtoms/QUIP)
To use this package you must have the QUIP libAatoms library available To use this package you must have the QUIP libAtoms library available
on your system. on your system.
[Author:] Albert Bartok (Cambridge University) [Author:] Albert Bartok (Cambridge University)
@ -2809,7 +2809,7 @@ USER-VTK package :link(USER-VTK),h4
A "dump vtk"_dump_vtk.html command which outputs snapshot info in the A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
"VTK format"_vtk, enabling visualization by "Paraview"_paraview or "VTK format"_vtk, enabling visualization by "Paraview"_paraview or
other visuzlization packages. other visualization packages.
:link(vtk,http://www.vtk.org) :link(vtk,http://www.vtk.org)
:link(paraview,http://www.paraview.org) :link(paraview,http://www.paraview.org)

26
doc/src/Section_start.txt
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@ -79,7 +79,7 @@ This section has the following sub-sections:
Read this first :h5,link(start_2_1) Read this first :h5,link(start_2_1)
If you want to avoid building LAMMPS yourself, read the preceeding If you want to avoid building LAMMPS yourself, read the preceding
section about options available for downloading and installing section about options available for downloading and installing
executables. Details are discussed on the "download"_download page. executables. Details are discussed on the "download"_download page.
@ -252,7 +252,7 @@ re-compile, after typing "make clean" (which will describe different
clean options). clean options).
The LMP_INC variable is used to include options that turn on ifdefs The LMP_INC variable is used to include options that turn on ifdefs
within the LAMMPS code. The options that are currently recogized are: within the LAMMPS code. The options that are currently recognized are:
-DLAMMPS_GZIP -DLAMMPS_GZIP
-DLAMMPS_JPEG -DLAMMPS_JPEG
@ -363,7 +363,7 @@ installed on your platform. If MPI is installed on your system in the
usual place (under /usr/local), you also may not need to specify these usual place (under /usr/local), you also may not need to specify these
3 variables, assuming /usr/local is in your path. On some large 3 variables, assuming /usr/local is in your path. On some large
parallel machines which use "modules" for their compile/link parallel machines which use "modules" for their compile/link
environements, you may simply need to include the correct module in environments, you may simply need to include the correct module in
your build environment, before building LAMMPS. Or the parallel your build environment, before building LAMMPS. Or the parallel
machine may have a vendor-provided MPI which the compiler has no machine may have a vendor-provided MPI which the compiler has no
trouble finding. trouble finding.
@ -431,7 +431,7 @@ use the KISS library described above.
You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables, You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
so the compiler and linker can find the needed FFT header and library so the compiler and linker can find the needed FFT header and library
files. Note that on some large parallel machines which use "modules" files. Note that on some large parallel machines which use "modules"
for their compile/link environements, you may simply need to include for their compile/link environments, you may simply need to include
the correct module in your build environment. Or the parallel machine the correct module in your build environment. Or the parallel machine
may have a vendor-provided FFT library which the compiler has no may have a vendor-provided FFT library which the compiler has no
trouble finding. See the src/MAKE/OPTIONS/Makefile.fftw file for an trouble finding. See the src/MAKE/OPTIONS/Makefile.fftw file for an
@ -470,7 +470,7 @@ precision.
The FFT_INC variable also allows for a -DFFT_SINGLE setting that will The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
use single-precision FFTs with PPPM, which can speed-up long-range use single-precision FFTs with PPPM, which can speed-up long-range
calulations, particularly in parallel or on GPUs. Fourier transform calculations, particularly in parallel or on GPUs. Fourier transform
and related PPPM operations are somewhat insensitive to floating point and related PPPM operations are somewhat insensitive to floating point
truncation errors and thus do not always need to be performed in truncation errors and thus do not always need to be performed in
double precision. Using the -DFFT_SINGLE setting trades off a little double precision. Using the -DFFT_SINGLE setting trades off a little
@ -483,7 +483,7 @@ with support for single-precision, as explained above. For FFTW3 you
also need to include -lfftw3f with the FFT_LIB setting, in addition to also need to include -lfftw3f with the FFT_LIB setting, in addition to
-lfftw3. For FFTW2, you also need to specify -DFFT_SIZE with the -lfftw3. For FFTW2, you also need to specify -DFFT_SIZE with the
FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of
-lfftw). Similarly, if FFTW2 has been preinstalled with an explicit -lfftw). Similarly, if FFTW2 has been pre-installed with an explicit
double-precision library (libdfftw.a and not the default libfftw.a), double-precision library (libdfftw.a and not the default libfftw.a),
then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify
-ldfftw to use double-precision FFTs. -ldfftw to use double-precision FFTs.
@ -714,7 +714,7 @@ list various make commands that can be used to manage packages.
If you use a command in a LAMMPS input script that is part of a If you use a command in a LAMMPS input script that is part of a
package, you must have built LAMMPS with that package, else you will package, you must have built LAMMPS with that package, else you will
get an error that the style is invalid or the command is unknown. get an error that the style is invalid or the command is unknown.
Every command's doc page specfies if it is part of a package. You can Every command's doc page specifies if it is part of a package. You can
type type
lmp_machine -h :pre lmp_machine -h :pre
@ -859,7 +859,7 @@ details for each package.
[External libraries:] [External libraries:]
Packages in the tables "Section 4"_Section_packages.html with an "ext" Packages in the tables "Section 4"_Section_packages.html with an "ext"
in the last column link to exernal libraries whose source code is not in the last column link to external libraries whose source code is not
included with LAMMPS. You must first download and install the library included with LAMMPS. You must first download and install the library
before building LAMMPS with that package installed. E.g. the voronoi before building LAMMPS with that package installed. E.g. the voronoi
package links to the freely available "Voro++ library"_voro_home2. You package links to the freely available "Voro++ library"_voro_home2. You
@ -963,7 +963,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
Obj_shared_foo. This is so that each file can be compiled with the Obj_shared_foo. This is so that each file can be compiled with the
-fPIC flag which is required for inclusion in a shared library. The -fPIC flag which is required for inclusion in a shared library. The
build will create the file liblammps_foo.so which another application build will create the file liblammps_foo.so which another application
can link to dyamically. It will also create a soft link liblammps.so, can link to dynamically. It will also create a soft link liblammps.so,
which will point to the most recently built shared library. This is which will point to the most recently built shared library. This is
the file the Python wrapper loads by default. the file the Python wrapper loads by default.
@ -1329,8 +1329,8 @@ LAMMPS is compiled with CUDA=yes.
numa Nm :pre numa Nm :pre
This option is only relevant when using pthreads with hwloc support. This option is only relevant when using pthreads with hwloc support.
In this case Nm defines the number of NUMA regions (typicaly sockets) In this case Nm defines the number of NUMA regions (typically sockets)
on a node which will be utilizied by a single MPI rank. By default Nm on a node which will be utilized by a single MPI rank. By default Nm
= 1. If this option is used the total number of worker-threads per = 1. If this option is used the total number of worker-threads per
MPI rank is threads*numa. Currently it is always almost better to MPI rank is threads*numa. Currently it is always almost better to
assign at least one MPI rank per NUMA region, and leave numa set to assign at least one MPI rank per NUMA region, and leave numa set to
@ -1394,7 +1394,7 @@ replica runs on on one or a few processors. Note that with MPI
installed on a machine (e.g. your desktop), you can run on more installed on a machine (e.g. your desktop), you can run on more
(virtual) processors than you have physical processors. (virtual) processors than you have physical processors.
To run multiple independent simulatoins from one input script, using To run multiple independent simulations from one input script, using
multiple partitions, see "Section 6.4"_Section_howto.html#howto_4 multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
of the manual. World- and universe-style "variables"_variable.html of the manual. World- and universe-style "variables"_variable.html
are useful in this context. are useful in this context.
@ -1673,7 +1673,7 @@ The first section provides a global loop timing summary. The {loop time}
is the total wall time for the section. The {Performance} line is is the total wall time for the section. The {Performance} line is
provided for convenience to help predicting the number of loop provided for convenience to help predicting the number of loop
continuations required and for comparing performance with other, continuations required and for comparing performance with other,
similar MD codes. The {CPU use} line provides the CPU utilzation per similar MD codes. The {CPU use} line provides the CPU utilization per
MPI task; it should be close to 100% times the number of OpenMP MPI task; it should be close to 100% times the number of OpenMP
threads (or 1 of no OpenMP). Lower numbers correspond to delays due threads (or 1 of no OpenMP). Lower numbers correspond to delays due
to file I/O or insufficient thread utilization. to file I/O or insufficient thread utilization.

2
doc/src/accelerate_intel.txt
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@ -78,7 +78,7 @@ order of operations compared to LAMMPS without acceleration:
Neighbor lists can be created in a different order :ulb,l Neighbor lists can be created in a different order :ulb,l
Bins used for sorting atoms can be oriented differently :l Bins used for sorting atoms can be oriented differently :l
The default stencil order for PPPM is 7. By default, LAMMPS will The default stencil order for PPPM is 7. By default, LAMMPS will
calculate other PPPM parameters to fit the desired acuracy with calculate other PPPM parameters to fit the desired accuracy with
this order :l this order :l
The {newton} setting applies to all atoms, not just atoms shared The {newton} setting applies to all atoms, not just atoms shared
between MPI tasks :l between MPI tasks :l

4
doc/src/compute_cluster_atom.txt
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@ -28,7 +28,7 @@ compute 1 all aggregate/atom 3.5 :pre
[Description:] [Description:]
Define a computation that assigns each atom a cluster, fragement, Define a computation that assigns each atom a cluster, fragment,
or aggregate ID. or aggregate ID.
A cluster is defined as a set of atoms, each of which is within the A cluster is defined as a set of atoms, each of which is within the
@ -53,7 +53,7 @@ like micelles.
Only atoms in the compute group are clustered and assigned cluster Only atoms in the compute group are clustered and assigned cluster
IDs. Atoms not in the compute group are assigned a cluster ID = 0. IDs. Atoms not in the compute group are assigned a cluster ID = 0.
For fragments, only bonds where [both] atoms of the bond are included For fragments, only bonds where [both] atoms of the bond are included
in the compute group are assigned to fragments, so that only fragmets in the compute group are assigned to fragments, so that only fragments
are detected where [all] atoms are in the compute group. Thus atoms are detected where [all] atoms are in the compute group. Thus atoms
may be included in the compute group, yes still have a fragment ID of 0. may be included in the compute group, yes still have a fragment ID of 0.

12
doc/src/compute_pressure_uef.txt
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@ -25,15 +25,15 @@ compute 2 all pressure/uef my_temp_uef virial :pre
[Description:] [Description:]
This command is used to compute the pressure tensor in This command is used to compute the pressure tensor in
the reference frame of the applied flow field when the reference frame of the applied flow field when
"fix nvt/uef"_fix_nh_uef.html" or "fix nvt/uef"_fix_nh_uef.html" or
"fix npt/uef"_fix_nh_uef.html" is used. "fix npt/uef"_fix_nh_uef.html" is used.
It is not necessary to use this command to compute the scalar It is not necessary to use this command to compute the scalar
value of the pressure. A "compute pressure"_compute_pressure.html value of the pressure. A "compute pressure"_compute_pressure.html
may be used for that purpose. may be used for that purpose.
The keywords and output information are documented in The keywords and output information are documented in
"compute_pressure"_compute_pressure.html. "compute_pressure"_compute_pressure.html.
[Restrictions:] [Restrictions:]
@ -46,8 +46,8 @@ This command can only be used when "fix nvt/uef"_fix_nh_uef.html
or "fix npt/uef"_fix_nh_uef.html is active. or "fix npt/uef"_fix_nh_uef.html is active.
The kinetic contribution to the pressure tensor The kinetic contribution to the pressure tensor
will be accurate only when will be accurate only when
the compute specificed by {temp-ID} is a the compute specified by {temp-ID} is a
"compute temp/uef"_compute_temp_uef.html. "compute temp/uef"_compute_temp_uef.html.
[Related commands:] [Related commands:]

6
doc/src/fix_halt.txt
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@ -64,10 +64,10 @@ not performed once every {N} steps by this command. Instead it is
performed (typically) only a small number of times and the elapsed performed (typically) only a small number of times and the elapsed
times are used to predict when the end-of-the-run will be. Both of times are used to predict when the end-of-the-run will be. Both of
these attributes can be useful when performing benchmark calculations these attributes can be useful when performing benchmark calculations
for a desired length of time with minmimal overhead. For example, if for a desired length of time with minimal overhead. For example, if
a run is performing 1000s of timesteps/sec, the overhead for syncing a run is performing 1000s of timesteps/sec, the overhead for syncing
the timer frequently across a large number of processors may be the timer frequently across a large number of processors may be
non-negligble. non-negligible.
Equal-style variables evaluate to a numeric value. See the Equal-style variables evaluate to a numeric value. See the
"variable"_variable.html command for a description. They calculate "variable"_variable.html command for a description. They calculate
@ -125,7 +125,7 @@ to the screen and logfile when the halt condition is triggered. If
{message} is set to yes, a one line message with the values that {message} is set to yes, a one line message with the values that
triggered the halt is printed. If {message} is set to no, no message triggered the halt is printed. If {message} is set to no, no message
is printed; the run simply exits. The latter may be desirable for is printed; the run simply exits. The latter may be desirable for
post-processing tools that extract thermodyanmic information from log post-processing tools that extract thermodynamic information from log
files. files.
[Restart, fix_modify, output, run start/stop, minimize info:] [Restart, fix_modify, output, run start/stop, minimize info:]

2
doc/src/fix_mvv_dpd.txt
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@ -44,7 +44,7 @@ the velocity for the force evaluation:
where the parameter <font size="4">&lambda;</font> depends on the where the parameter <font size="4">&lambda;</font> depends on the
specific choice of DPD parameters, and needs to be tuned on a specific choice of DPD parameters, and needs to be tuned on a
case-by-case basis. Specification of a {lambda} value is opttional. case-by-case basis. Specification of a {lambda} value is optional.
If specified, the setting must be from 0.0 to 1.0. If not specified, 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 a default value of 0.5 is used, which effectively reproduces the
standard velocity-Verlet (VV) scheme. For more details, see standard velocity-Verlet (VV) scheme. For more details, see

4
doc/src/fix_neb.txt
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@ -113,9 +113,9 @@ keeping the replicas equally spaced.
:line :line
The keyword {perp} specifies if and how a perpendicual nudging force The keyword {perp} specifies if and how a perpendicular nudging force
is computed. It adds a spring force perpendicular to the path in is computed. It adds a spring force perpendicular to the path in
order to prevent the path from becoming too kinky. It can order to prevent the path from becoming too strongly kinked. It can
significantly improve the convergence of the NEB calculation when the significantly improve the convergence of the NEB calculation when the
resolution is poor. I.e. when few replicas are used; see resolution is poor. I.e. when few replicas are used; see
"(Maras)"_#Maras1 for details. "(Maras)"_#Maras1 for details.

10
doc/src/neb.txt
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@ -322,9 +322,9 @@ the fix neb command.
The forward (reverse) energy barrier is the potential energy of the The forward (reverse) energy barrier is the potential energy of the
highest replica minus the energy of the first (last) replica. highest replica minus the energy of the first (last) replica.
Supplementary informations for all replicas can be printed out to the Supplementary information for all replicas can be printed out to the
screen and master log.lammps file by adding the verbose keyword. These screen and master log.lammps file by adding the verbose keyword. This
informations include the following. The "path angle" (pathangle) for information include the following. The "path angle" (pathangle) for
the replica i which is the angle between the 3N-length vectors (Ri-1 - the replica i which is the angle between the 3N-length vectors (Ri-1 -
Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica
i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are
@ -339,8 +339,8 @@ energy gradient of image i. ReplicaForce is the two-norm of the
3N-length force vector (including nudging forces) for replica i. 3N-length force vector (including nudging forces) for replica i.
MaxAtomForce is the maximum force component of any atom in replica i. MaxAtomForce is the maximum force component of any atom in replica i.
When a NEB calculation does not converge properly, these suplementary When a NEB calculation does not converge properly, the suplementary
informations can help understanding what is going wrong. For instance information can help understanding what is going wrong. For instance
when the path angle becomes accute the definition of tangent used in when the path angle becomes accute the definition of tangent used in
the NEB calculation is questionable and the NEB cannot may diverge the NEB calculation is questionable and the NEB cannot may diverge
"(Maras)"_#Maras2. "(Maras)"_#Maras2.

21
doc/utils/converters/lammpsdoc/txt2rst.py
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@ -148,15 +148,18 @@ class RSTFormatting(Formatting):
return "\n----------\n\n" + content.strip() return "\n----------\n\n" + content.strip()
def image(self, content, file, link=None): def image(self, content, file, link=None):
if link and (link.lower().endswith('.jpg') or # 2017-12-07: commented out to disable thumbnail processing due to dropping
link.lower().endswith('.jpeg') or # support for obsolete sphinxcontrib.images extension
link.lower().endswith('.png') or #
link.lower().endswith('.gif')): #if link and (link.lower().endswith('.jpg') or
converted = ".. thumbnail:: " + self.markup.unescape_rst_chars(link) + "\n" # link.lower().endswith('.jpeg') or
else: # link.lower().endswith('.png') or
converted = ".. image:: " + self.markup.unescape_rst_chars(file) + "\n" # link.lower().endswith('.gif')):
if link: # converted = ".. thumbnail:: " + self.markup.unescape_rst_chars(link) + "\n"
converted += " :target: " + self.markup.unescape_rst_chars(link) + "\n" #else:
converted = ".. image:: " + self.markup.unescape_rst_chars(file) + "\n"
if link:
converted += " :target: " + self.markup.unescape_rst_chars(link) + "\n"
if "c" in self.current_command_list: if "c" in self.current_command_list:
converted += " :align: center\n" converted += " :align: center\n"

5
doc/utils/sphinx-config/conf.py
View File

@ -31,8 +31,11 @@ import os
# ones. # ones.
extensions = [ extensions = [
'sphinx.ext.mathjax', 'sphinx.ext.mathjax',
'sphinxcontrib.images',
] ]
# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
# yet we can no longer use Sphinx 15.x, since that breaks with
# newer version of the multiprocessor module.
# 'sphinxcontrib.images',
images_config = { images_config = {
'default_image_width' : '25%', 'default_image_width' : '25%',