lmp = lammps() # create a LAMMPS object using the default liblammps.so library
-lmp = lammps(ptr=lmpptr) # ditto, but use lmpptr as previously created LAMMPS object
-lmp = lammps("g++") # create a LAMMPS object using the liblammps_g++.so library
-lmp = lammps("",list) # ditto, with command-line args, e.g. list = ["-echo","screen"]
-lmp = lammps("g++",list)
+lmp = lammps() # create a LAMMPS object using the default liblammps.so library
+ 4 optional args are allowed: name, cmdargs, ptr, comm
+lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
+lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
+lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library
+lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = ["-echo","screen"]
lmp.close() # destroy a LAMMPS object
@@ -706,8 +772,8 @@ argument.
returned, which you can use via normal Python subscripting. See the
extract() method in the src/atom.cpp file for a list of valid names.
Again, new names could easily be added. A pointer to a vector of
-doubles or integers, or a pointer to an array of doubles (double **)
-or integers (int **) is returned. You need to specify the appropriate
+doubles or integers, or a pointer to an array of doubles (double **)
+or integers (int **) is returned. You need to specify the appropriate
data type via the type argument.
For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is
@@ -802,8 +868,8 @@ own scripts, send them to us and we can include them in the LAMMPS
distribution.
-
-
+
+
| trivial.py |
@@ -813,19 +879,25 @@ distribution.
invoke various LAMMPS library interface routines |
| simple.py |
-mimic operation of couple/simple/simple.cpp in Python |
+run in parallel |
-| gui.py |
-GUI go/stop/temperature-slider to control LAMMPS |
+
| similar to examples/COUPLE/simple/simple.cpp |
+split.py |
-| plot.py |
-real-time temeperature plot with GnuPlot via Pizza.py |
+
| same as simple.py but running in parallel on a subset of procs |
+gui.py |
-| viz_tool.py |
-real-time viz via some viz package |
+
| GUI go/stop/temperature-slider to control LAMMPS |
+plot.py |
-| vizplotgui_tool.py |
-combination of viz_tool.py and plot.py and gui.py |
+
| real-time temeperature plot with GnuPlot via Pizza.py |
+viz_tool.py |
+
+| real-time viz via some viz package |
+vizplotgui_tool.py |
+
+| combination of viz_tool.py and plot.py and gui.py |
+ |
diff --git a/doc/Section_python.txt b/doc/Section_python.txt
index 67dc88e468..f9bfd2c291 100644
--- a/doc/Section_python.txt
+++ b/doc/Section_python.txt
@@ -303,10 +303,18 @@ incomplete and I had trouble with their installation. It's not clear
if some of the packages are still being actively developed and
supported.
-The one I recommend, since I have successfully used it with LAMMPS, is
-Pypar. Pypar requires the ubiquitous "Numpy
-package"_http://numpy.scipy.org be installed in your Python. After
-launching python, type
+The packages Pypar and mpi4py have both been successfully tested with
+LAMMPS. Pypar is simpler and easy to set up and use, but supports
+only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
+bit more complex to use. As of version 2.0.0, mpi4py is the only
+python MPI wrapper that allows passing a custom MPI communicator to
+the LAMMPS constructor, which means one can easily run one or more
+LAMMPS instances on subsets of the total MPI ranks.
+
+:line
+
+Pypar requires the ubiquitous "Numpy package"_http://numpy.scipy.org
+be installed in your Python. After launching Python, type
import numpy :pre
@@ -361,6 +369,51 @@ the right one.
:line
+To install mpi4py (version mpi4py-2.0.0 as of Oct 2015), unpack it
+and from its main directory, type
+
+python setup.py build
+sudo python setup.py install :pre
+
+Again, the "sudo" is only needed if required to copy mpi4py files into
+your Python distribution's site-packages directory. To install with
+user privilege into the user local directory type
+
+python setup.py install --user :pre
+
+If you have successully installed mpi4py, you should be able to run
+Python and type
+
+from mpi4py import MPI :pre
+
+without error. You should also be able to run python in parallel
+on a simple test script
+
+% mpirun -np 4 python test.py :pre
+
+where test.py contains the lines
+
+from mpi4py import MPI
+comm = MPI.COMM_WORLD
+print "Proc %d out of %d procs" % (comm.Get_rank(),comm.Get_size()) :pre
+
+and see one line of output for each processor you run on.
+
+IMPORTANT NOTE: To use mpi4py and LAMMPS in parallel from Python, you
+must insure both are using the same version of MPI. If you only have
+one MPI installed on your system, this is not an issue, but it can be
+if you have multiple MPIs. Your LAMMPS build is explicit about which
+MPI it is using, since you specify the details in your lo-level
+src/MAKE/Makefile.foo file. Mpi4py uses the "mpicc" command to find
+information about the MPI it uses to build against. And it tries to
+load "libmpi.so" from the LD_LIBRARY_PATH. This may or may not find
+the MPI library that LAMMPS is using. If you have problems running
+both mpi4py and LAMMPS together, this is an issue you may need to
+address, e.g. by moving other MPI installations so that mpi4py finds
+the right one.
+
+:line
+
11.6 Testing the Python-LAMMPS interface :link(py_6),h4
To test if LAMMPS is callable from Python, launch Python interactively
@@ -413,8 +466,8 @@ lmp_g++ -in in.lj :pre
[Test LAMMPS and Python in parallel:] :h5
To run LAMMPS in parallel, assuming you have installed the
-"Pypar"_http://datamining.anu.edu.au/~ole/pypar package as discussed
-above, create a test.py file containing these lines:
+"Pypar"_Pypar package as discussed above, create a test.py file
+containing these lines:
import pypar
from lammps import lammps
@@ -423,7 +476,20 @@ lmp.file("in.lj")
print "Proc %d out of %d procs has" % (pypar.rank(),pypar.size()),lmp
pypar.finalize() :pre
-You can then run it in parallel as:
+To run LAMMPS in parallel, assuming you have installed the
+"mpi4py"_mpi4py package as discussed above, create a test.py file
+containing these lines:
+
+from mpi4py import MPI
+from lammps import lammps
+lmp = lammps()
+lmp.file("in.lj")
+me = MPI.COMM_WORLD.Get_rank()
+nprocs = MPI.COMM_WORLD.Get_size()
+print "Proc %d out of %d procs has" % (me,nprocs),lmp
+MPI.Finalize() :pre
+
+You can either script in parallel as:
% mpirun -np 4 python test.py :pre
@@ -491,10 +557,11 @@ correspond one-to-one with calls you can make to the LAMMPS library
from a C++ or C or Fortran program.
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
-lmp = lammps(ptr=lmpptr) # ditto, but use lmpptr as previously created LAMMPS object
-lmp = lammps("g++") # create a LAMMPS object using the liblammps_g++.so library
-lmp = lammps("",list) # ditto, with command-line args, e.g. list = \["-echo","screen"\]
-lmp = lammps("g++",list) :pre
+ 4 optional args are allowed: name, cmdargs, ptr, comm
+lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
+lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
+lmp = lammps(name="g++") # create a LAMMPS object using the liblammps_g++.so library
+lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. list = \["-echo","screen"\] :pre
lmp.close() # destroy a LAMMPS object :pre
@@ -717,7 +784,8 @@ distribution.
trivial.py, read/run a LAMMPS input script thru Python,
demo.py, invoke various LAMMPS library interface routines,
-simple.py, mimic operation of couple/simple/simple.cpp in Python,
+simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
+split.py, same as simple.py but running in parallel on a subset of procs,
gui.py, GUI go/stop/temperature-slider to control LAMMPS,
plot.py, real-time temeperature plot with GnuPlot via Pizza.py,
viz_tool.py, real-time viz via some viz package,
diff --git a/doc/_images/angle_dipole_couple.jpg b/doc/_images/angle_dipole_couple.jpg
new file mode 100644
index 0000000000..f16849b2f9
Binary files /dev/null and b/doc/_images/angle_dipole_couple.jpg differ
diff --git a/doc/_images/hexorder.jpg b/doc/_images/hexorder.jpg
new file mode 100644
index 0000000000..dafa25cabe
Binary files /dev/null and b/doc/_images/hexorder.jpg differ
diff --git a/doc/_images/orientorder.jpg b/doc/_images/orientorder.jpg
new file mode 100644
index 0000000000..5ec79964f0
Binary files /dev/null and b/doc/_images/orientorder.jpg differ
diff --git a/doc/angle_dipole.html b/doc/angle_dipole.html
index 5367f273fc..6c78a4e535 100644
--- a/doc/angle_dipole.html
+++ b/doc/angle_dipole.html
@@ -159,15 +159,17 @@ and the reference (bond) vector r_ij:
angle.
The torque on the dipole can be obtained by differentiating the
potential using the ‘chain rule’ as in appendix C.3 of
-(Allen):
+
(Allen):
Example: if gamma0 is set to 0 degrees, the torque generated by
the potential will tend to align the dipole along the reference
direction defined by the (bond) vector r_ij (in other words, mu_j is
restrained to point towards atom ‘i’).
-
Note that the angle dipole potential does not give rise to any force,
-because it does not depend on the distance between i and j (it only
-depends on the angle between mu_j and r_ij).
+
The dipolar torque T_j must be counterbalanced in order to conserve
+the local angular momentum. This is achieved via an additional force
+couple generating a torque equivalent to the opposite of T_j:
+
+
where F_i and F_j are applied on atoms i and j, respectively.
The following coefficients must be defined for each angle type via the
angle_coeff command as in the example above, or in
the data file or restart files read by the read_data
diff --git a/doc/angle_dipole.txt b/doc/angle_dipole.txt
index 7585c82658..6ca68c5942 100644
--- a/doc/angle_dipole.txt
+++ b/doc/angle_dipole.txt
@@ -50,9 +50,13 @@ the potential will tend to align the dipole along the reference
direction defined by the (bond) vector r_ij (in other words, mu_j is
restrained to point towards atom 'i').
-Note that the angle dipole potential does not give rise to any force,
-because it does not depend on the distance between i and j (it only
-depends on the angle between mu_j and r_ij).
+The dipolar torque T_j must be counterbalanced in order to conserve
+the local angular momentum. This is achieved via an additional force
+couple generating a torque equivalent to the opposite of T_j:
+
+:c,image(Eqs/angle_dipole_couple.jpg)
+
+where F_i and F_j are applied on atoms i and j, respectively.
The following coefficients must be defined for each angle type via the
"angle_coeff"_angle_coeff.html command as in the example above, or in
diff --git a/doc/compute_temp_drude.html b/doc/compute_temp_drude.html
index ddc47ddcd6..b8b8ab808d 100644
--- a/doc/compute_temp_drude.html
+++ b/doc/compute_temp_drude.html
@@ -145,8 +145,7 @@
Description
Define a computation that calculates the temperatures of core-Drude
-pairs. This compute is designed to be used with the thermalized Drude
-oscillator model. This compute is designed to be used with the
+pairs. This compute is designed to be used with the
thermalized Drude oscillator model. Polarizable
models in LAMMPS are described in this Section.
Drude oscillators consist of a core particle and a Drude particle
@@ -189,7 +188,7 @@ assumed to be constant for the duration of the run unless the
diff --git a/doc/compute_temp_drude.txt b/doc/compute_temp_drude.txt
index 8b0755999c..47f0702d51 100644
--- a/doc/compute_temp_drude.txt
+++ b/doc/compute_temp_drude.txt
@@ -22,8 +22,7 @@ compute TDRUDE all temp/drude :pre
[Description:]
Define a computation that calculates the temperatures of core-Drude
-pairs. This compute is designed to be used with the thermalized Drude
-oscillator model. This compute is designed to be used with the
+pairs. This compute is designed to be used with the
"thermalized Drude oscillator model"_tutorial_drude.html. Polarizable
models in LAMMPS are described in "this
Section"_Section_howto.html#howto_25.
@@ -75,7 +74,7 @@ assumed to be constant for the duration of the run unless the
[Related commands:]
"fix drude"_fix_drude.html, "fix
-langevin_drude"_fix_langevin_drude.html, "fix
+langevin/drude"_fix_langevin_drude.html, "fix
drude/transform"_fix_drude_transform.html, "pair_style
thole"_pair_thole.html, "compute temp"_compute_temp.html
diff --git a/doc/doc2/Eqs/.log b/doc/doc2/Eqs/.log
deleted file mode 100644
index 39ba97a0d2..0000000000
--- a/doc/doc2/Eqs/.log
+++ /dev/null
@@ -1,30 +0,0 @@
-This is TeX, Version 3.14159 (Web2C 7.4.5) (format=latex 2008.11.14) 27 AUG 2011 15:16
-**pair_sph_tait
-(/usr/share/texmf/tex/latex/tools/.tex
-LaTeX2e <2001/06/01>
-Babel
and hyphenation patterns for american, french, german, ngerman, n
-ohyphenation, loaded.
-File ignored)
-*
-(Please type a command or say `\end')
-*x
-
-! LaTeX Error: Missing \begin{document}.
-
-See the LaTeX manual or LaTeX Companion for explanation.
-Type H for immediate help.
- ...
-
-<*> x
-
-? x
-
-Here is how much of TeX's memory you used:
- 6 strings out of 95847
- 257 string characters out of 1195947
- 44507 words of memory out of 1000001
- 3034 multiletter control sequences out of 10000+50000
- 3640 words of font info for 14 fonts, out of 500000 for 1000
- 14 hyphenation exceptions out of 1000
- 5i,0n,4p,93b,14s stack positions out of 1500i,500n,5000p,200000b,5000s
-No pages of output.
diff --git a/doc/doc2/Eqs/angle_charmm.jpg b/doc/doc2/Eqs/angle_charmm.jpg
deleted file mode 100644
index c6e6c297d2..0000000000
Binary files a/doc/doc2/Eqs/angle_charmm.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_charmm.tex b/doc/doc2/Eqs/angle_charmm.tex
deleted file mode 100644
index 00b37ba335..0000000000
--- a/doc/doc2/Eqs/angle_charmm.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K (\theta - \theta_0)^2 + K_{UB} (r - r_{UB})^2
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_class2.jpg b/doc/doc2/Eqs/angle_class2.jpg
deleted file mode 100644
index f0f2a5152e..0000000000
Binary files a/doc/doc2/Eqs/angle_class2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_class2.tex b/doc/doc2/Eqs/angle_class2.tex
deleted file mode 100644
index e5a542e87a..0000000000
--- a/doc/doc2/Eqs/angle_class2.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E & = & E_a + E_{bb} + E_{ba} \\
- E_a & = & K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4 \\
- E_{bb} & = & M (r_{ij} - r_1) (r_{jk} - r_2) \\
- E_{ba} & = & N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2 (r_{jk} - r_2) (\theta - \theta_0)
-\end{eqnarray*}
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_cosine.jpg b/doc/doc2/Eqs/angle_cosine.jpg
deleted file mode 100644
index 23b9b64310..0000000000
Binary files a/doc/doc2/Eqs/angle_cosine.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_cosine.tex b/doc/doc2/Eqs/angle_cosine.tex
deleted file mode 100644
index e766676099..0000000000
--- a/doc/doc2/Eqs/angle_cosine.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K [1 + \cos(\theta)]
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_cosine_delta.jpg b/doc/doc2/Eqs/angle_cosine_delta.jpg
deleted file mode 100644
index c6e90bb2c5..0000000000
Binary files a/doc/doc2/Eqs/angle_cosine_delta.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_cosine_delta.tex b/doc/doc2/Eqs/angle_cosine_delta.tex
deleted file mode 100644
index 918e9e5046..0000000000
--- a/doc/doc2/Eqs/angle_cosine_delta.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K [1 - \cos(\theta - \theta_0)]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/angle_cosine_periodic.jpg b/doc/doc2/Eqs/angle_cosine_periodic.jpg
deleted file mode 100644
index a9d7d50cb3..0000000000
Binary files a/doc/doc2/Eqs/angle_cosine_periodic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_cosine_periodic.tex b/doc/doc2/Eqs/angle_cosine_periodic.tex
deleted file mode 100644
index 69aa1bba6a..0000000000
--- a/doc/doc2/Eqs/angle_cosine_periodic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=C\left[ 1-B(-1)^ncos\left( n\theta\right) \right]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/angle_cosine_shift.jpg b/doc/doc2/Eqs/angle_cosine_shift.jpg
deleted file mode 100644
index d9929939c8..0000000000
Binary files a/doc/doc2/Eqs/angle_cosine_shift.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_cosine_shift.tex b/doc/doc2/Eqs/angle_cosine_shift.tex
deleted file mode 100644
index e795d6beff..0000000000
--- a/doc/doc2/Eqs/angle_cosine_shift.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-\frac{Umin}{2} \left[ 1+Cos(\theta-\theta_0) \right]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/angle_cosine_shift_exp.jpg b/doc/doc2/Eqs/angle_cosine_shift_exp.jpg
deleted file mode 100644
index 294986de4b..0000000000
Binary files a/doc/doc2/Eqs/angle_cosine_shift_exp.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_cosine_shift_exp.tex b/doc/doc2/Eqs/angle_cosine_shift_exp.tex
deleted file mode 100644
index 4afa01356c..0000000000
--- a/doc/doc2/Eqs/angle_cosine_shift_exp.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-U_{min}
-\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
-\quad\mbox{with}\quad
-U(\theta,\theta_0)
-=-0.5 \left(1+\cos(\theta-\theta_0) \right)
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/angle_cosine_squared.jpg b/doc/doc2/Eqs/angle_cosine_squared.jpg
deleted file mode 100644
index b992398b7d..0000000000
Binary files a/doc/doc2/Eqs/angle_cosine_squared.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_cosine_squared.tex b/doc/doc2/Eqs/angle_cosine_squared.tex
deleted file mode 100644
index 57ae47ae45..0000000000
--- a/doc/doc2/Eqs/angle_cosine_squared.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K [\cos(\theta) - \cos(\theta_0)]^2
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_dipole_gamma.jpg b/doc/doc2/Eqs/angle_dipole_gamma.jpg
deleted file mode 100644
index 4bf618e252..0000000000
Binary files a/doc/doc2/Eqs/angle_dipole_gamma.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_dipole_gamma.tex b/doc/doc2/Eqs/angle_dipole_gamma.tex
deleted file mode 100644
index 965b74ad96..0000000000
--- a/doc/doc2/Eqs/angle_dipole_gamma.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- \cos\gamma = \frac{\vec{\mu_j}\bullet\vec{r_{ij}}}{\mu_j\,r_{ij}}
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_dipole_potential.jpg b/doc/doc2/Eqs/angle_dipole_potential.jpg
deleted file mode 100644
index b1285e8957..0000000000
Binary files a/doc/doc2/Eqs/angle_dipole_potential.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_dipole_potential.tex b/doc/doc2/Eqs/angle_dipole_potential.tex
deleted file mode 100644
index 8949835eb7..0000000000
--- a/doc/doc2/Eqs/angle_dipole_potential.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K (\cos\gamma - \cos\gamma_0)^2
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_dipole_torque.jpg b/doc/doc2/Eqs/angle_dipole_torque.jpg
deleted file mode 100644
index 996a9df3cb..0000000000
Binary files a/doc/doc2/Eqs/angle_dipole_torque.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_dipole_torque.tex b/doc/doc2/Eqs/angle_dipole_torque.tex
deleted file mode 100644
index 9527459fdc..0000000000
--- a/doc/doc2/Eqs/angle_dipole_torque.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\,
- \vec{r_{ij}} \times \vec{\mu_j}
-$$
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_fourier.jpg b/doc/doc2/Eqs/angle_fourier.jpg
deleted file mode 100644
index e748e67430..0000000000
Binary files a/doc/doc2/Eqs/angle_fourier.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_fourier.tex b/doc/doc2/Eqs/angle_fourier.tex
deleted file mode 100644
index f7f76462e3..0000000000
--- a/doc/doc2/Eqs/angle_fourier.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K [C_0 + C_1 \cos ( \theta) + C_2 \cos( 2 \theta) ]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/angle_fourier_simple.jpg b/doc/doc2/Eqs/angle_fourier_simple.jpg
deleted file mode 100644
index 6c9297b970..0000000000
Binary files a/doc/doc2/Eqs/angle_fourier_simple.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_fourier_simple.tex b/doc/doc2/Eqs/angle_fourier_simple.tex
deleted file mode 100644
index 3228315a13..0000000000
--- a/doc/doc2/Eqs/angle_fourier_simple.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K [ 1.0 + c \cos ( n \theta) ]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/angle_harmonic.jpg b/doc/doc2/Eqs/angle_harmonic.jpg
deleted file mode 100644
index 352be0b544..0000000000
Binary files a/doc/doc2/Eqs/angle_harmonic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_harmonic.tex b/doc/doc2/Eqs/angle_harmonic.tex
deleted file mode 100644
index c566376b5b..0000000000
--- a/doc/doc2/Eqs/angle_harmonic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K (\theta - \theta_0)^2
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/angle_quartic.jpg b/doc/doc2/Eqs/angle_quartic.jpg
deleted file mode 100644
index 744ce7a35f..0000000000
Binary files a/doc/doc2/Eqs/angle_quartic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/angle_quartic.tex b/doc/doc2/Eqs/angle_quartic.tex
deleted file mode 100644
index ff9ff9a7dc..0000000000
--- a/doc/doc2/Eqs/angle_quartic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K_2 (\theta - \theta_0)^2 + K_3 (\theta - \theta_0)^3 + K_4 (\theta - \theta_0)^4
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/bond_class2.jpg b/doc/doc2/Eqs/bond_class2.jpg
deleted file mode 100644
index 493048100e..0000000000
Binary files a/doc/doc2/Eqs/bond_class2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/bond_class2.tex b/doc/doc2/Eqs/bond_class2.tex
deleted file mode 100644
index 0735b61025..0000000000
--- a/doc/doc2/Eqs/bond_class2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_fene.jpg b/doc/doc2/Eqs/bond_fene.jpg
deleted file mode 100644
index e8b909c08f..0000000000
Binary files a/doc/doc2/Eqs/bond_fene.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/bond_fene.tex b/doc/doc2/Eqs/bond_fene.tex
deleted file mode 100644
index ec4dd8efa2..0000000000
--- a/doc/doc2/Eqs/bond_fene.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
- 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_fene_expand.jpg b/doc/doc2/Eqs/bond_fene_expand.jpg
deleted file mode 100644
index 1d04acec32..0000000000
Binary files a/doc/doc2/Eqs/bond_fene_expand.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/bond_fene_expand.tex b/doc/doc2/Eqs/bond_fene_expand.tex
deleted file mode 100644
index 5fd96e7ad5..0000000000
--- a/doc/doc2/Eqs/bond_fene_expand.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = -0.5 K R_0^2
- \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] +
- 4 \epsilon \left[ \left(\frac{\sigma}{\left(r -
- \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r -
- \Delta\right)}\right)^6 \right] + \epsilon
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/bond_harmonic.jpg b/doc/doc2/Eqs/bond_harmonic.jpg
deleted file mode 100644
index fe9ef5619b..0000000000
Binary files a/doc/doc2/Eqs/bond_harmonic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/bond_harmonic.tex b/doc/doc2/Eqs/bond_harmonic.tex
deleted file mode 100644
index 2461086898..0000000000
--- a/doc/doc2/Eqs/bond_harmonic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K (r - r_0)^2
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_harmonic_shift.jpg b/doc/doc2/Eqs/bond_harmonic_shift.jpg
deleted file mode 100644
index 3e66d853a5..0000000000
Binary files a/doc/doc2/Eqs/bond_harmonic_shift.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/bond_harmonic_shift.tex b/doc/doc2/Eqs/bond_harmonic_shift.tex
deleted file mode 100644
index 3daa16724f..0000000000
--- a/doc/doc2/Eqs/bond_harmonic_shift.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_harmonic_shift_cut.jpg b/doc/doc2/Eqs/bond_harmonic_shift_cut.jpg
deleted file mode 100644
index 06640e4fe0..0000000000
Binary files a/doc/doc2/Eqs/bond_harmonic_shift_cut.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/bond_harmonic_shift_cut.tex b/doc/doc2/Eqs/bond_harmonic_shift_cut.tex
deleted file mode 100644
index 3daa16724f..0000000000
--- a/doc/doc2/Eqs/bond_harmonic_shift_cut.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_morse.jpg b/doc/doc2/Eqs/bond_morse.jpg
deleted file mode 100644
index 6795c9e527..0000000000
Binary files a/doc/doc2/Eqs/bond_morse.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/bond_morse.tex b/doc/doc2/Eqs/bond_morse.tex
deleted file mode 100644
index a0d7a89961..0000000000
--- a/doc/doc2/Eqs/bond_morse.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2
- E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_nonlinear.jpg b/doc/doc2/Eqs/bond_nonlinear.jpg
deleted file mode 100644
index 0f18d8e73f..0000000000
Binary files a/doc/doc2/Eqs/bond_nonlinear.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/bond_nonlinear.tex b/doc/doc2/Eqs/bond_nonlinear.tex
deleted file mode 100644
index b8cdc96169..0000000000
--- a/doc/doc2/Eqs/bond_nonlinear.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/bond_quartic.jpg b/doc/doc2/Eqs/bond_quartic.jpg
deleted file mode 100644
index 9d092883b2..0000000000
Binary files a/doc/doc2/Eqs/bond_quartic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/bond_quartic.tex b/doc/doc2/Eqs/bond_quartic.tex
deleted file mode 100644
index 0d0cceb353..0000000000
--- a/doc/doc2/Eqs/bond_quartic.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
- 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/box.jpg b/doc/doc2/Eqs/box.jpg
deleted file mode 100644
index 4cb43df953..0000000000
Binary files a/doc/doc2/Eqs/box.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/box.tex b/doc/doc2/Eqs/box.tex
deleted file mode 100644
index 8442ea85b6..0000000000
--- a/doc/doc2/Eqs/box.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-a &=& {\rm lx} \\
-b^2 &=& {\rm ly}^2 + {\rm xy}^2 \\
-c^2 &=& {\rm lz}^2 + {\rm xz}^2 + {\rm yz}^2 \\
-\cos{\alpha} &=& \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
-\cos{\beta} &=& \frac{\rm xz}{c} \\
-\cos{\gamma} &=& \frac{\rm xy}{b} \\
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/box_inverse.jpg b/doc/doc2/Eqs/box_inverse.jpg
deleted file mode 100644
index 5d0895b87e..0000000000
Binary files a/doc/doc2/Eqs/box_inverse.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/box_inverse.tex b/doc/doc2/Eqs/box_inverse.tex
deleted file mode 100644
index 68994f2868..0000000000
--- a/doc/doc2/Eqs/box_inverse.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-{\rm lx} &=& a \\
-{\rm xy} &=& b \cos{\gamma} \\
-{\rm xz} &=& c \cos{\beta}\\
-{\rm ly}^2 &=& b^2 - {\rm xy}^2 \\
-{\rm yz} &=& \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
-{\rm lz}^2 &=& c^2 - {\rm xz}^2 - {\rm yz}^2 \\
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/centro_symmetry.jpg b/doc/doc2/Eqs/centro_symmetry.jpg
deleted file mode 100644
index 1e89d11a11..0000000000
Binary files a/doc/doc2/Eqs/centro_symmetry.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/centro_symmetry.tex b/doc/doc2/Eqs/centro_symmetry.tex
deleted file mode 100644
index 8d9a9a33e6..0000000000
--- a/doc/doc2/Eqs/centro_symmetry.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- CS = \sum_{i = 1}^{N/2} | \vec{R}_i + \vec{R}_{i+N/2} |^2
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/cna_cutoff1.jpg b/doc/doc2/Eqs/cna_cutoff1.jpg
deleted file mode 100644
index fae5c6b636..0000000000
Binary files a/doc/doc2/Eqs/cna_cutoff1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/cna_cutoff1.tex b/doc/doc2/Eqs/cna_cutoff1.tex
deleted file mode 100644
index 782082bdfd..0000000000
--- a/doc/doc2/Eqs/cna_cutoff1.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
- r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
- r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
- r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/cna_cutoff2.jpg b/doc/doc2/Eqs/cna_cutoff2.jpg
deleted file mode 100644
index 744b61e9b4..0000000000
Binary files a/doc/doc2/Eqs/cna_cutoff2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/cna_cutoff2.tex b/doc/doc2/Eqs/cna_cutoff2.tex
deleted file mode 100644
index 7559441a2c..0000000000
--- a/doc/doc2/Eqs/cna_cutoff2.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
- Rc + Rs > 2*{\rm cutoff}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_bar.jpg b/doc/doc2/Eqs/compute_fep_bar.jpg
deleted file mode 100644
index 772ec9c045..0000000000
Binary files a/doc/doc2/Eqs/compute_fep_bar.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_fep_bar.tex b/doc/doc2/Eqs/compute_fep_bar.tex
deleted file mode 100644
index a40aa1c297..0000000000
--- a/doc/doc2/Eqs/compute_fep_bar.tex
+++ /dev/null
@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /kT \right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 + \Delta_0^1A \right) /kT \right]} \right>_1 \]
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_fdti.jpg b/doc/doc2/Eqs/compute_fep_fdti.jpg
deleted file mode 100644
index ae8de241cc..0000000000
Binary files a/doc/doc2/Eqs/compute_fep_fdti.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_fep_fdti.tex b/doc/doc2/Eqs/compute_fep_fdti.tex
deleted file mode 100644
index fdea6faa3d..0000000000
--- a/doc/doc2/Eqs/compute_fep_fdti.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left( \frac{\partial
- A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda
-\approx \sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) -
- A(\lambda_i)}{\delta} \]
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_fep.jpg b/doc/doc2/Eqs/compute_fep_fep.jpg
deleted file mode 100644
index d84a76b0dd..0000000000
Binary files a/doc/doc2/Eqs/compute_fep_fep.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_fep_fep.tex b/doc/doc2/Eqs/compute_fep_fep.tex
deleted file mode 100644
index 718aad3c40..0000000000
--- a/doc/doc2/Eqs/compute_fep_fep.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A =
-- kT \sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) -
- U(\lambda_i)}{kT} \right) \right>_{\lambda_i} \]
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_lambda.jpg b/doc/doc2/Eqs/compute_fep_lambda.jpg
deleted file mode 100644
index 5ef9e8b9f2..0000000000
Binary files a/doc/doc2/Eqs/compute_fep_lambda.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_fep_lambda.tex b/doc/doc2/Eqs/compute_fep_lambda.tex
deleted file mode 100644
index 08c8faaa3c..0000000000
--- a/doc/doc2/Eqs/compute_fep_lambda.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- \lambda = 0 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_0 \\
- \lambda = 1 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_1
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_ti.jpg b/doc/doc2/Eqs/compute_fep_ti.jpg
deleted file mode 100644
index 6b0c8fdc19..0000000000
Binary files a/doc/doc2/Eqs/compute_fep_ti.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_fep_ti.tex b/doc/doc2/Eqs/compute_fep_ti.tex
deleted file mode 100644
index 6222dbd503..0000000000
--- a/doc/doc2/Eqs/compute_fep_ti.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left< \frac{\partial
- U(\lambda)}{\partial\lambda} \right>_\lambda \mathrm{d}\lambda
-\approx \sum_{i=0}^{n-1} w_i \left< \frac{U(\lambda_{i} + \delta) -
- U(\lambda_i)}{\delta} \right>_{\lambda_i} \]
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_u.jpg b/doc/doc2/Eqs/compute_fep_u.jpg
deleted file mode 100644
index 62df5dd0c0..0000000000
Binary files a/doc/doc2/Eqs/compute_fep_u.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_fep_u.tex b/doc/doc2/Eqs/compute_fep_u.tex
deleted file mode 100644
index e847a9ac44..0000000000
--- a/doc/doc2/Eqs/compute_fep_u.tex
+++ /dev/null
@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ U(\lambda) = U_{\mathrm{bg}} + U_1(\lambda) + U_0(\lambda) \]
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_fep_vol.jpg b/doc/doc2/Eqs/compute_fep_vol.jpg
deleted file mode 100644
index a66facad39..0000000000
Binary files a/doc/doc2/Eqs/compute_fep_vol.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_fep_vol.tex b/doc/doc2/Eqs/compute_fep_vol.tex
deleted file mode 100644
index 0301e39788..0000000000
--- a/doc/doc2/Eqs/compute_fep_vol.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
- \frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right)
-\right>_{\lambda_i}}{\left< V \right>_{\lambda_i}} \]
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_gyration.jpg b/doc/doc2/Eqs/compute_gyration.jpg
deleted file mode 100644
index 2285444434..0000000000
Binary files a/doc/doc2/Eqs/compute_gyration.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_gyration.tex b/doc/doc2/Eqs/compute_gyration.tex
deleted file mode 100644
index 97204f1ded..0000000000
--- a/doc/doc2/Eqs/compute_gyration.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/compute_msd_nongauss.jpg b/doc/doc2/Eqs/compute_msd_nongauss.jpg
deleted file mode 100644
index d57f6a4af8..0000000000
Binary files a/doc/doc2/Eqs/compute_msd_nongauss.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_msd_nongauss.tex b/doc/doc2/Eqs/compute_msd_nongauss.tex
deleted file mode 100644
index 168d8f72ed..0000000000
--- a/doc/doc2/Eqs/compute_msd_nongauss.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_saed1.jpg b/doc/doc2/Eqs/compute_saed1.jpg
deleted file mode 100644
index 6bad3a6104..0000000000
Binary files a/doc/doc2/Eqs/compute_saed1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_saed1.tex b/doc/doc2/Eqs/compute_saed1.tex
deleted file mode 100644
index 0db2f55ecd..0000000000
--- a/doc/doc2/Eqs/compute_saed1.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- I=\frac{F^{*}F}{N}
-$$
-
-\end{document}
-
diff --git a/doc/doc2/Eqs/compute_saed2.jpg b/doc/doc2/Eqs/compute_saed2.jpg
deleted file mode 100644
index 2b3b0bc090..0000000000
Binary files a/doc/doc2/Eqs/compute_saed2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_saed2.tex b/doc/doc2/Eqs/compute_saed2.tex
deleted file mode 100644
index d005602339..0000000000
--- a/doc/doc2/Eqs/compute_saed2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
-$$
-\end{document}
-
diff --git a/doc/doc2/Eqs/compute_saed3.jpg b/doc/doc2/Eqs/compute_saed3.jpg
deleted file mode 100644
index 1bbc920908..0000000000
Binary files a/doc/doc2/Eqs/compute_saed3.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_saed3.tex b/doc/doc2/Eqs/compute_saed3.tex
deleted file mode 100644
index 5988a620c7..0000000000
--- a/doc/doc2/Eqs/compute_saed3.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5}
-a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )
-$$
-\end{document}
-
diff --git a/doc/doc2/Eqs/compute_sna_atom1.jpg b/doc/doc2/Eqs/compute_sna_atom1.jpg
deleted file mode 100644
index fe4b641aa6..0000000000
Binary files a/doc/doc2/Eqs/compute_sna_atom1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_sna_atom1.tex b/doc/doc2/Eqs/compute_sna_atom1.tex
deleted file mode 100644
index 93e2709bf9..0000000000
--- a/doc/doc2/Eqs/compute_sna_atom1.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-\theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom2.jpg b/doc/doc2/Eqs/compute_sna_atom2.jpg
deleted file mode 100644
index 7a4b2c2111..0000000000
Binary files a/doc/doc2/Eqs/compute_sna_atom2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_sna_atom2.tex b/doc/doc2/Eqs/compute_sna_atom2.tex
deleted file mode 100644
index 98d8f2efa6..0000000000
--- a/doc/doc2/Eqs/compute_sna_atom2.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)}
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom3.jpg b/doc/doc2/Eqs/compute_sna_atom3.jpg
deleted file mode 100644
index 41d6774e9c..0000000000
Binary files a/doc/doc2/Eqs/compute_sna_atom3.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_sna_atom3.tex b/doc/doc2/Eqs/compute_sna_atom3.tex
deleted file mode 100644
index 5e3212f7bd..0000000000
--- a/doc/doc2/Eqs/compute_sna_atom3.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\newcommand{\hcoeff}[9]{H\!\!{\tiny\begin{array}{l}#1 #2 #3 \\ #4 #5 #6 \\ #7 #8 #9 \end{array}}}
-
-\begin{equation}
-B_{j_1,j_2,j} = \\
-\sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^*
-\hcoeff{j}{m}{m'}{j_1}{\!m_1}{\!m'_1}{j_2}{m_2}{m'_2}
-u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2}
-\end{equation}
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom4.jpg b/doc/doc2/Eqs/compute_sna_atom4.jpg
deleted file mode 100644
index 5d53943bf4..0000000000
Binary files a/doc/doc2/Eqs/compute_sna_atom4.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_sna_atom4.tex b/doc/doc2/Eqs/compute_sna_atom4.tex
deleted file mode 100644
index 3477d163e3..0000000000
--- a/doc/doc2/Eqs/compute_sna_atom4.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-\label{eqn:f_c}
-f_c(r) & = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\
-& = & 0, r > R_{ii'}
-\end{eqnarray*}
-
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom5.jpg b/doc/doc2/Eqs/compute_sna_atom5.jpg
deleted file mode 100644
index 732731fe13..0000000000
Binary files a/doc/doc2/Eqs/compute_sna_atom5.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_sna_atom5.tex b/doc/doc2/Eqs/compute_sna_atom5.tex
deleted file mode 100644
index 72f5a0fe7c..0000000000
--- a/doc/doc2/Eqs/compute_sna_atom5.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-
-\begin{equation}
-- \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j} }}{\partial {\bf r}_i}
-\end{equation}
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_sna_atom6.jpg b/doc/doc2/Eqs/compute_sna_atom6.jpg
deleted file mode 100644
index 963dd81416..0000000000
Binary files a/doc/doc2/Eqs/compute_sna_atom6.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_sna_atom6.tex b/doc/doc2/Eqs/compute_sna_atom6.tex
deleted file mode 100644
index 7da589548b..0000000000
--- a/doc/doc2/Eqs/compute_sna_atom6.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-
-\begin{eqnarray*}
-- {\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i}
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/compute_xrd1.jpg b/doc/doc2/Eqs/compute_xrd1.jpg
deleted file mode 100644
index 8432fad4aa..0000000000
Binary files a/doc/doc2/Eqs/compute_xrd1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_xrd1.tex b/doc/doc2/Eqs/compute_xrd1.tex
deleted file mode 100644
index 6e749c768d..0000000000
--- a/doc/doc2/Eqs/compute_xrd1.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- I=Lp(\theta)\frac{F^{*}F}{N}
-$$
-
-\end{document}
-
diff --git a/doc/doc2/Eqs/compute_xrd2.jpg b/doc/doc2/Eqs/compute_xrd2.jpg
deleted file mode 100644
index 1bcf0494ea..0000000000
Binary files a/doc/doc2/Eqs/compute_xrd2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_xrd2.tex b/doc/doc2/Eqs/compute_xrd2.tex
deleted file mode 100644
index d005602339..0000000000
--- a/doc/doc2/Eqs/compute_xrd2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
-$$
-\end{document}
-
diff --git a/doc/doc2/Eqs/compute_xrd3.jpg b/doc/doc2/Eqs/compute_xrd3.jpg
deleted file mode 100644
index 19f7aa99b5..0000000000
Binary files a/doc/doc2/Eqs/compute_xrd3.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_xrd3.tex b/doc/doc2/Eqs/compute_xrd3.tex
deleted file mode 100644
index da0254134c..0000000000
--- a/doc/doc2/Eqs/compute_xrd3.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- Lp(\theta)=\frac{1+cos^{2}(2\theta)}{cos(\theta)sin^{2}(\theta)}
-$$
-\end{document}
-
diff --git a/doc/doc2/Eqs/compute_xrd4.jpg b/doc/doc2/Eqs/compute_xrd4.jpg
deleted file mode 100644
index 385bb1efd7..0000000000
Binary files a/doc/doc2/Eqs/compute_xrd4.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_xrd4.tex b/doc/doc2/Eqs/compute_xrd4.tex
deleted file mode 100644
index d4deb7ca55..0000000000
--- a/doc/doc2/Eqs/compute_xrd4.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- \frac{sin(\theta)}{\lambda}=\frac{\left | \mathbf{k} \right |}{2}
-$$
-\end{document}
-
diff --git a/doc/doc2/Eqs/compute_xrd5.jpg b/doc/doc2/Eqs/compute_xrd5.jpg
deleted file mode 100644
index c6f0a2609a..0000000000
Binary files a/doc/doc2/Eqs/compute_xrd5.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/compute_xrd5.tex b/doc/doc2/Eqs/compute_xrd5.tex
deleted file mode 100644
index 2d97a3288b..0000000000
--- a/doc/doc2/Eqs/compute_xrd5.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4}
-a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )+c
-$$
-\end{document}
-
diff --git a/doc/doc2/Eqs/dihedral_charmm.jpg b/doc/doc2/Eqs/dihedral_charmm.jpg
deleted file mode 100644
index 810afa3cd2..0000000000
Binary files a/doc/doc2/Eqs/dihedral_charmm.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_charmm.tex b/doc/doc2/Eqs/dihedral_charmm.tex
deleted file mode 100644
index c3d860b265..0000000000
--- a/doc/doc2/Eqs/dihedral_charmm.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K [ 1 + \cos (n \phi - d) ]
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_class2.jpg b/doc/doc2/Eqs/dihedral_class2.jpg
deleted file mode 100644
index 6a6780e769..0000000000
Binary files a/doc/doc2/Eqs/dihedral_class2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_class2.tex b/doc/doc2/Eqs/dihedral_class2.tex
deleted file mode 100644
index 02acc16fb9..0000000000
--- a/doc/doc2/Eqs/dihedral_class2.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E & = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\
- E_d & = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\
- E_{mbt} & = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\
- E_{ebt} & = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\
- & & (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\
- E_{at} & = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\
- & & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\
- E_{aat} & = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\
- E_{bb13} & = & N (r_{ij} - r_1) (r_{kl} - r_3)
-\end{eqnarray*}
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_cosine_shift_exp.jpg b/doc/doc2/Eqs/dihedral_cosine_shift_exp.jpg
deleted file mode 100644
index ea0a7550f8..0000000000
Binary files a/doc/doc2/Eqs/dihedral_cosine_shift_exp.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_cosine_shift_exp.tex b/doc/doc2/Eqs/dihedral_cosine_shift_exp.tex
deleted file mode 100644
index 4afa01356c..0000000000
--- a/doc/doc2/Eqs/dihedral_cosine_shift_exp.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-U_{min}
-\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
-\quad\mbox{with}\quad
-U(\theta,\theta_0)
-=-0.5 \left(1+\cos(\theta-\theta_0) \right)
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/dihedral_fourier.jpg b/doc/doc2/Eqs/dihedral_fourier.jpg
deleted file mode 100644
index 663ac17ee6..0000000000
Binary files a/doc/doc2/Eqs/dihedral_fourier.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_fourier.tex b/doc/doc2/Eqs/dihedral_fourier.tex
deleted file mode 100644
index 960d3a8ea8..0000000000
--- a/doc/doc2/Eqs/dihedral_fourier.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \sum_{i=1,m} K_i [ 1.0 + \cos ( n_i \phi - d_i ) ]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/dihedral_harmonic.jpg b/doc/doc2/Eqs/dihedral_harmonic.jpg
deleted file mode 100644
index cb5c16a8ca..0000000000
Binary files a/doc/doc2/Eqs/dihedral_harmonic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_harmonic.tex b/doc/doc2/Eqs/dihedral_harmonic.tex
deleted file mode 100644
index 9d02036fcc..0000000000
--- a/doc/doc2/Eqs/dihedral_harmonic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K [ 1 + d \cos (n \phi) ]
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_helix.jpg b/doc/doc2/Eqs/dihedral_helix.jpg
deleted file mode 100644
index 01a0ec982c..0000000000
Binary files a/doc/doc2/Eqs/dihedral_helix.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_helix.tex b/doc/doc2/Eqs/dihedral_helix.tex
deleted file mode 100644
index ae25776f2c..0000000000
--- a/doc/doc2/Eqs/dihedral_helix.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] +
- C [1 + \cos(\theta + \frac{\pi}{4})]
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_multi_harmonic.jpg b/doc/doc2/Eqs/dihedral_multi_harmonic.jpg
deleted file mode 100644
index d066cd212b..0000000000
Binary files a/doc/doc2/Eqs/dihedral_multi_harmonic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_multi_harmonic.tex b/doc/doc2/Eqs/dihedral_multi_harmonic.tex
deleted file mode 100644
index 819aa7c57c..0000000000
--- a/doc/doc2/Eqs/dihedral_multi_harmonic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \sum_{n=1,5} A_n \cos^{n-1}(\phi)
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_nharmonic.jpg b/doc/doc2/Eqs/dihedral_nharmonic.jpg
deleted file mode 100644
index 4f4928bdd5..0000000000
Binary files a/doc/doc2/Eqs/dihedral_nharmonic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_nharmonic.tex b/doc/doc2/Eqs/dihedral_nharmonic.tex
deleted file mode 100644
index 57a1d25284..0000000000
--- a/doc/doc2/Eqs/dihedral_nharmonic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \sum_{n=1,n} A_n \cos^{n-1}(\phi)
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/dihedral_opls.jpg b/doc/doc2/Eqs/dihedral_opls.jpg
deleted file mode 100644
index 0546aebfde..0000000000
Binary files a/doc/doc2/Eqs/dihedral_opls.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_opls.tex b/doc/doc2/Eqs/dihedral_opls.tex
deleted file mode 100644
index 5e4aada53a..0000000000
--- a/doc/doc2/Eqs/dihedral_opls.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] +
- \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)]
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/dihedral_quadratic.jpg b/doc/doc2/Eqs/dihedral_quadratic.jpg
deleted file mode 100644
index 8fb17622f8..0000000000
Binary files a/doc/doc2/Eqs/dihedral_quadratic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dihedral_quadratic.tex b/doc/doc2/Eqs/dihedral_quadratic.tex
deleted file mode 100644
index 049e4b2ec4..0000000000
--- a/doc/doc2/Eqs/dihedral_quadratic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K (\phi - \phi_0)^2
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/dihedral_sign.jpg b/doc/doc2/Eqs/dihedral_sign.jpg
deleted file mode 100644
index 8d8352e8fc..0000000000
Binary files a/doc/doc2/Eqs/dihedral_sign.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/dreiding_hbond.jpg b/doc/doc2/Eqs/dreiding_hbond.jpg
deleted file mode 100644
index 76cc42a45b..0000000000
Binary files a/doc/doc2/Eqs/dreiding_hbond.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_ECP1.jpg b/doc/doc2/Eqs/eff_ECP1.jpg
deleted file mode 100644
index 3b8a3f8ff3..0000000000
Binary files a/doc/doc2/Eqs/eff_ECP1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_ECP1.tex b/doc/doc2/Eqs/eff_ECP1.tex
deleted file mode 100644
index 7eecad0b8d..0000000000
--- a/doc/doc2/Eqs/eff_ECP1.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E_{Pauli(ECP_s)}=p_1\exp\left(-\frac{p_2r^2}{p_3+s^2} \right)
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/eff_ECP2.jpg b/doc/doc2/Eqs/eff_ECP2.jpg
deleted file mode 100644
index 195ed55e43..0000000000
Binary files a/doc/doc2/Eqs/eff_ECP2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_ECP2.tex b/doc/doc2/Eqs/eff_ECP2.tex
deleted file mode 100644
index 238fe2f4f0..0000000000
--- a/doc/doc2/Eqs/eff_ECP2.tex
+++ /dev/null
@@ -1,8 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E_{Pauli(ECP_p)}=p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right]
-$$
-
\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/eff_KE.jpg b/doc/doc2/Eqs/eff_KE.jpg
deleted file mode 100644
index 40eed0df65..0000000000
Binary files a/doc/doc2/Eqs/eff_KE.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_KE.tex b/doc/doc2/Eqs/eff_KE.tex
deleted file mode 100644
index 9f9af2fa25..0000000000
--- a/doc/doc2/Eqs/eff_KE.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E_{KE} = \frac{\hbar^2 }{{m_{e} }}\sum\limits_i {\frac{3}{{2s_i^2 }}}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/eff_NN.jpg b/doc/doc2/Eqs/eff_NN.jpg
deleted file mode 100644
index c3c52e19b4..0000000000
Binary files a/doc/doc2/Eqs/eff_NN.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_NN.tex b/doc/doc2/Eqs/eff_NN.tex
deleted file mode 100644
index 4f9bb6d132..0000000000
--- a/doc/doc2/Eqs/eff_NN.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E_{NN} = \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i < j} {\frac{{Z_i Z_j }}{{R_{ij} }}}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/eff_Ne.jpg b/doc/doc2/Eqs/eff_Ne.jpg
deleted file mode 100644
index e23ceacc88..0000000000
Binary files a/doc/doc2/Eqs/eff_Ne.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_Ne.tex b/doc/doc2/Eqs/eff_Ne.tex
deleted file mode 100644
index e6813b125c..0000000000
--- a/doc/doc2/Eqs/eff_Ne.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E_{Ne} = - \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i,j} {\frac{{Z_i }}{{R_{ij} }}Erf\left( {\frac{{\sqrt 2 R_{ij} }}{{s_j }}} \right)}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/eff_Pauli.jpg b/doc/doc2/Eqs/eff_Pauli.jpg
deleted file mode 100644
index 61bb8652e3..0000000000
Binary files a/doc/doc2/Eqs/eff_Pauli.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_Pauli.tex b/doc/doc2/Eqs/eff_Pauli.tex
deleted file mode 100644
index b6b8070cc7..0000000000
--- a/doc/doc2/Eqs/eff_Pauli.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E_{Pauli} = \sum\limits_{\sigma _i = \sigma _j } {E\left( { \uparrow \uparrow } \right)_{ij}} + \sum\limits_{\sigma _i \ne \sigma _j } {E\left( { \uparrow \downarrow } \right)_{ij}}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/eff_ee.jpg b/doc/doc2/Eqs/eff_ee.jpg
deleted file mode 100644
index aef84d0fd4..0000000000
Binary files a/doc/doc2/Eqs/eff_ee.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_ee.tex b/doc/doc2/Eqs/eff_ee.tex
deleted file mode 100644
index 5d17e5557b..0000000000
--- a/doc/doc2/Eqs/eff_ee.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E_{ee} = \frac{1}{{4\pi \varepsilon _0 }}\sum\limits_{i < j} {\frac{1}{{r_{ij} }}Erf\left( {\frac{{\sqrt 2 r_{ij} }}{{\sqrt {s_i^2 + s_j^2 } }}} \right)}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/eff_energy_expression.gif b/doc/doc2/Eqs/eff_energy_expression.gif
deleted file mode 100644
index 70cc4ddbc7..0000000000
Binary files a/doc/doc2/Eqs/eff_energy_expression.gif and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_energy_expression.jpg b/doc/doc2/Eqs/eff_energy_expression.jpg
deleted file mode 100644
index e06fe8ff2f..0000000000
Binary files a/doc/doc2/Eqs/eff_energy_expression.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/eff_energy_expression.tex b/doc/doc2/Eqs/eff_energy_expression.tex
deleted file mode 100644
index f56380f646..0000000000
--- a/doc/doc2/Eqs/eff_energy_expression.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-U\left(R,r,s\right) = E_{NN} \left( R \right) + E_{Ne} \left( {R,r,s} \right) + E_{ee} \left( {r,s} \right) + E_{KE} \left( {r,s} \right) + E_{PR} \left( { \uparrow \downarrow ,S} \right)
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_box_relax1.jpg b/doc/doc2/Eqs/fix_box_relax1.jpg
deleted file mode 100644
index d425526046..0000000000
Binary files a/doc/doc2/Eqs/fix_box_relax1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_box_relax1.tex b/doc/doc2/Eqs/fix_box_relax1.tex
deleted file mode 100644
index a332360666..0000000000
--- a/doc/doc2/Eqs/fix_box_relax1.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E = U + P_t \left(V-V_0 \right) + E_{strain}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_box_relax2.jpg b/doc/doc2/Eqs/fix_box_relax2.jpg
deleted file mode 100644
index 8fac42e0fa..0000000000
Binary files a/doc/doc2/Eqs/fix_box_relax2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_box_relax2.tex b/doc/doc2/Eqs/fix_box_relax2.tex
deleted file mode 100644
index bc9cddef4e..0000000000
--- a/doc/doc2/Eqs/fix_box_relax2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\mathbf P = P_t \mathbf I + {\mathbf S_t} \left( \mathbf h_0^{-1} \right)^t \mathbf h_{0d}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_gld1.jpg b/doc/doc2/Eqs/fix_gld1.jpg
deleted file mode 100644
index d54ce57a6c..0000000000
Binary files a/doc/doc2/Eqs/fix_gld1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_gld1.tex b/doc/doc2/Eqs/fix_gld1.tex
deleted file mode 100644
index baa0f32a5b..0000000000
--- a/doc/doc2/Eqs/fix_gld1.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{align*}
- &{\bf F}_{j}(t) = {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\
- &\Gamma_j(t-s) = \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\
- &\langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = \text{k$_\text{B}$T} ~\Gamma_j(t-s)
-\end{align*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_lb_fluid_boltzmann.jpg b/doc/doc2/Eqs/fix_lb_fluid_boltzmann.jpg
deleted file mode 100644
index 9d82b40ecb..0000000000
Binary files a/doc/doc2/Eqs/fix_lb_fluid_boltzmann.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_lb_fluid_boltzmann.tex b/doc/doc2/Eqs/fix_lb_fluid_boltzmann.tex
deleted file mode 100755
index 4a6ca6fe01..0000000000
--- a/doc/doc2/Eqs/fix_lb_fluid_boltzmann.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\left(\partial_t + e_{i\alpha}\partial_{\alpha}\right)f_i = -\frac{1}{\tau}\left(f_i - f_i^{eq}\right) + W_i
-$$
-
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_lb_fluid_fluidforce.jpg b/doc/doc2/Eqs/fix_lb_fluid_fluidforce.jpg
deleted file mode 100644
index d3149616ca..0000000000
Binary files a/doc/doc2/Eqs/fix_lb_fluid_fluidforce.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_lb_fluid_fluidforce.tex b/doc/doc2/Eqs/fix_lb_fluid_fluidforce.tex
deleted file mode 100755
index 8433c9264a..0000000000
--- a/doc/doc2/Eqs/fix_lb_fluid_fluidforce.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-{\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha}
-$$
-
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_lb_fluid_gammadefault.jpg b/doc/doc2/Eqs/fix_lb_fluid_gammadefault.jpg
deleted file mode 100644
index cd10239c9b..0000000000
Binary files a/doc/doc2/Eqs/fix_lb_fluid_gammadefault.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_lb_fluid_gammadefault.tex b/doc/doc2/Eqs/fix_lb_fluid_gammadefault.tex
deleted file mode 100755
index 1af82c4972..0000000000
--- a/doc/doc2/Eqs/fix_lb_fluid_gammadefault.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\gamma = \frac{2m_um_v}{m_u+m_v}\left(\frac{1}{\Delta t_{collision}}\right)
-$$
-
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_lb_fluid_navierstokes.jpg b/doc/doc2/Eqs/fix_lb_fluid_navierstokes.jpg
deleted file mode 100644
index 0a1c104141..0000000000
Binary files a/doc/doc2/Eqs/fix_lb_fluid_navierstokes.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex b/doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex
deleted file mode 100755
index 41ca4674e9..0000000000
--- a/doc/doc2/Eqs/fix_lb_fluid_navierstokes.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\partial_t \rho + \partial_{\beta}\left(\rho u_{\beta}\right)= 0
-$$
-$$
-\partial_t\left(\rho u_{\alpha}\right) + \partial_{\beta}\left(\rho u_{\alpha} u_{\beta}\right) = \partial_{\beta}\sigma_{\alpha \beta} + F_{\alpha} + \partial_{\beta}\left(\eta_{\alpha \beta \gamma \nu}\partial_{\gamma} u_{\nu}\right)
-$$
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_lb_fluid_properties.jpg b/doc/doc2/Eqs/fix_lb_fluid_properties.jpg
deleted file mode 100644
index 3d70cd7667..0000000000
Binary files a/doc/doc2/Eqs/fix_lb_fluid_properties.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_lb_fluid_properties.tex b/doc/doc2/Eqs/fix_lb_fluid_properties.tex
deleted file mode 100755
index fe1290be12..0000000000
--- a/doc/doc2/Eqs/fix_lb_fluid_properties.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\rho = \displaystyle\sum\limits_{i} f_i
-$$
-$$
-\rho u_{\alpha} = \displaystyle\sum\limits_{i} f_i e_{i\alpha}
-$$
-
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_lb_fluid_stress.jpg b/doc/doc2/Eqs/fix_lb_fluid_stress.jpg
deleted file mode 100644
index 8f730e9d70..0000000000
Binary files a/doc/doc2/Eqs/fix_lb_fluid_stress.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_lb_fluid_stress.tex b/doc/doc2/Eqs/fix_lb_fluid_stress.tex
deleted file mode 100755
index b4e0982536..0000000000
--- a/doc/doc2/Eqs/fix_lb_fluid_stress.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\sigma_{\alpha \beta} = -P_{\alpha \beta} = -\rho a_0 \delta_{\alpha \beta}
-$$
-
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_lb_fluid_viscosity.jpg b/doc/doc2/Eqs/fix_lb_fluid_viscosity.jpg
deleted file mode 100644
index 1816317ee6..0000000000
Binary files a/doc/doc2/Eqs/fix_lb_fluid_viscosity.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_lb_fluid_viscosity.tex b/doc/doc2/Eqs/fix_lb_fluid_viscosity.tex
deleted file mode 100755
index d5925f213f..0000000000
--- a/doc/doc2/Eqs/fix_lb_fluid_viscosity.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\eta_{\alpha \beta \gamma \nu} = \eta\left[\delta_{\alpha \gamma}\delta_{\beta \nu} + \delta_{\alpha \nu}\delta_{\beta \gamma} - \frac{2}{3}\delta_{\alpha \beta}\delta_{\gamma \nu}\right] + \Lambda \delta_{\alpha \beta}\delta_{\gamma \nu}
-$$
-
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_nh1.jpg b/doc/doc2/Eqs/fix_nh1.jpg
deleted file mode 100644
index db59dbc43e..0000000000
Binary files a/doc/doc2/Eqs/fix_nh1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_nh1.tex b/doc/doc2/Eqs/fix_nh1.tex
deleted file mode 100644
index f6928495ce..0000000000
--- a/doc/doc2/Eqs/fix_nh1.tex
+++ /dev/null
@@ -1,35 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-\Huge
-
-\begin{document}
-
-\mathchardef\mhyphen="2D
-
-% The imaginary unit
-\providecommand*{\iu}%
- {\ensuremath{{\rm i}}}
-
-
-\begin{eqnarray*}
-\exp \left(\iu{} L \Delta t \right) &=&
-\exp \left(\iu{} L_{\rm T\mhyphen baro} \frac{\Delta t}{2} \right)
-\exp \left(\iu{} L_{\rm T\mhyphen part} \frac{\Delta t}{2} \right)
-\exp \left(\iu{} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
-\exp \left(\iu{} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\
-&&\times \left[
-\exp \left(\iu{} L_{2}^{(1)} \frac{\Delta t}{2n} \right)
-\exp \left(\iu{} L_{\epsilon , 1} \frac{\Delta t}{n} \right)
-\exp \left(\iu{} L_1 \frac{\Delta t}{n} \right)
-\exp \left(\iu{} L_{2}^{(1)} \frac{\Delta t}{2n} \right)
-\right]^n \\
-&&\times
-\exp \left(\iu{} L_{2}^{(2)} \frac{\Delta t}{2} \right)
-\exp \left(\iu{} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
-\exp \left(\iu{} L_{\rm T\mhyphen part} \frac{\Delta t}{2} \right)
-\exp \left(\iu{} L_{\rm T\mhyphen baro} \frac{\Delta t}{2} \right) \\
-&&+ \mathcal{O} \left(\Delta t^3 \right)
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_nphug.jpg b/doc/doc2/Eqs/fix_nphug.jpg
deleted file mode 100644
index a3a67e7b7b..0000000000
Binary files a/doc/doc2/Eqs/fix_nphug.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_nphug.tex b/doc/doc2/Eqs/fix_nphug.tex
deleted file mode 100644
index 4e162b69b7..0000000000
--- a/doc/doc2/Eqs/fix_nphug.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-T_t - T = \frac{\left(\frac{1}{2}\left(P + P_0\right)\left(V_0 - V\right) + E_0 - E\right)}{N_{dof} k_B } = Delta
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_orient_fcc.jpg b/doc/doc2/Eqs/fix_orient_fcc.jpg
deleted file mode 100644
index b22e6c9c20..0000000000
Binary files a/doc/doc2/Eqs/fix_orient_fcc.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_orient_fcc.tex b/doc/doc2/Eqs/fix_orient_fcc.tex
deleted file mode 100644
index 5596848eb5..0000000000
--- a/doc/doc2/Eqs/fix_orient_fcc.tex
+++ /dev/null
@@ -1,30 +0,0 @@
-\newcommand{\br}{\mathbf{r}}
-
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{equation}
- \xi_{i} = \sum_{j=1}^{12} \left| \br_{j} - \br_{j}^{\rm I} \right|
-\end{equation}
-
-\begin{equation}
- \xi_{\rm IJ} = \sum_{j=1}^{12} \left| \br_{j}^{\rm J} - \br_{j}^{\rm I} \right|
-\end{equation}
-
-\begin{eqnarray}
- \xi_{\rm low} &=& {\rm cutlo} \, \xi_{\rm IJ} \\
- \xi_{\rm high} &=& {\rm cuthi} \, \xi_{\rm IJ}
-\end{eqnarray}
-
-\begin{eqnarray}
- \omega_{i} &=& \frac{\pi}{2}
- \frac{\xi_{i} - \xi_{\rm low}}{\xi_{\rm high} - \xi_{\rm low}} \\
- \mbox{\hspace*{72pt}} \nonumber \\
- u_{i} &=& 0 \mbox{\hspace{84pt} for } \xi_{i} < \xi_{\rm low} \nonumber \\
- &=& {\rm dE}\,\frac{1 - \cos(2 \omega_{i})}{2}
- \mbox{\hspace{10pt} for } \xi_{\rm low} < \xi_{i} < \xi_{\rm high} \\
- &=& {\rm dE} \mbox{\hspace{80pt} for } \xi_{\rm high} < \xi_{i}
- \nonumber
-\end{eqnarray}
-\end{document}
diff --git a/doc/doc2/Eqs/fix_pimd.jpg b/doc/doc2/Eqs/fix_pimd.jpg
deleted file mode 100644
index b6e8f5831b..0000000000
Binary files a/doc/doc2/Eqs/fix_pimd.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_pimd.tex b/doc/doc2/Eqs/fix_pimd.tex
deleted file mode 100644
index 983fead8e4..0000000000
--- a/doc/doc2/Eqs/fix_pimd.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- Z = \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ]
-$$
-
-$$
- H_{eff} = \bigg(\sum_{i=1}^P \frac{p_i^2}{2m_i}\bigg) + V_{eff}
-$$
-
-$$
- V_{eff} = \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_rattle_constraints.jpg b/doc/doc2/Eqs/fix_rattle_constraints.jpg
deleted file mode 100644
index 2ba86095cd..0000000000
Binary files a/doc/doc2/Eqs/fix_rattle_constraints.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_rattle_constraints.tex b/doc/doc2/Eqs/fix_rattle_constraints.tex
deleted file mode 100644
index daff0ce775..0000000000
--- a/doc/doc2/Eqs/fix_rattle_constraints.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-\usepackage{amsmath}
-
-\begin{document}
-\begin{align*}
-\mathbf r^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= d^2_{ij} \quad \text{and} \\
-\mathbf v^{n+1}_{ij} \cdot \mathbf r^{n+1}_{ij} &= 0, \label{eq:velcon}
-\end{align*}
-\end{document}
diff --git a/doc/doc2/Eqs/fix_rattle_rij.jpg b/doc/doc2/Eqs/fix_rattle_rij.jpg
deleted file mode 100644
index b08e2fe02e..0000000000
Binary files a/doc/doc2/Eqs/fix_rattle_rij.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_rattle_rij.tex b/doc/doc2/Eqs/fix_rattle_rij.tex
deleted file mode 100644
index fae0457c60..0000000000
--- a/doc/doc2/Eqs/fix_rattle_rij.tex
+++ /dev/null
@@ -1,8 +0,0 @@
-\documentclass[12pt]{article}
-\usepackage{amsmath}
-\begin{document}
-$$
- \mathbf r^{n+1}_{ij} = \mathbf r^n_j - \mathbf r^n_i
-$$
-\end{document}
-
diff --git a/doc/doc2/Eqs/fix_spring_rg.jpg b/doc/doc2/Eqs/fix_spring_rg.jpg
deleted file mode 100644
index 313844f555..0000000000
Binary files a/doc/doc2/Eqs/fix_spring_rg.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_spring_rg.tex b/doc/doc2/Eqs/fix_spring_rg.tex
deleted file mode 100644
index b772aaf652..0000000000
--- a/doc/doc2/Eqs/fix_spring_rg.tex
+++ /dev/null
@@ -1,19 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-{R_G}^2 = \frac{1}{M}\sum_{i}^{N}{m_{i}\left( x_{i} -
-\frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right)^{2}}
-$$
-
-$$
- E = K\left( R_G - R_{G0} \right)^{2}
-$$
-
-$$
-F_{i} = 2K\frac{m_{i}}{M}\left( 1-\frac{R_{G0}}{R_G}
-\right)\left( x_{i} - \frac{1}{M}\sum_{j}^{N}{m_{j}x_{j}} \right)
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/fix_ti_rs_force.jpg b/doc/doc2/Eqs/fix_ti_rs_force.jpg
deleted file mode 100644
index a09bcb66c5..0000000000
Binary files a/doc/doc2/Eqs/fix_ti_rs_force.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ti_rs_force.tex b/doc/doc2/Eqs/fix_ti_rs_force.tex
deleted file mode 100644
index 849c0ccc97..0000000000
--- a/doc/doc2/Eqs/fix_ti_rs_force.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
- F_{\text{total}} = \lambda F_{\text{int}}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_rs_function_1.jpg b/doc/doc2/Eqs/fix_ti_rs_function_1.jpg
deleted file mode 100644
index 478dc5781d..0000000000
Binary files a/doc/doc2/Eqs/fix_ti_rs_function_1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ti_rs_function_1.tex b/doc/doc2/Eqs/fix_ti_rs_function_1.tex
deleted file mode 100644
index 033d8d7559..0000000000
--- a/doc/doc2/Eqs/fix_ti_rs_function_1.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- \lambda(\tau) = \lambda_i + \tau \left( \lambda_f - \lambda_i \right)
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_rs_function_2.jpg b/doc/doc2/Eqs/fix_ti_rs_function_2.jpg
deleted file mode 100644
index 4fbfe45c63..0000000000
Binary files a/doc/doc2/Eqs/fix_ti_rs_function_2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ti_rs_function_2.tex b/doc/doc2/Eqs/fix_ti_rs_function_2.tex
deleted file mode 100644
index a1dd377dcc..0000000000
--- a/doc/doc2/Eqs/fix_ti_rs_function_2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- \lambda(\tau) = \frac{\lambda_i}{1 + \tau \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_rs_function_3.jpg b/doc/doc2/Eqs/fix_ti_rs_function_3.jpg
deleted file mode 100644
index 94ab0f468c..0000000000
Binary files a/doc/doc2/Eqs/fix_ti_rs_function_3.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ti_rs_function_3.tex b/doc/doc2/Eqs/fix_ti_rs_function_3.tex
deleted file mode 100644
index 2d2790fa97..0000000000
--- a/doc/doc2/Eqs/fix_ti_rs_function_3.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- \lambda(\tau) = \frac{\lambda_i}{ 1 + \log_2(1+\tau) \left( \frac{\lambda_i}{\lambda_f} - 1 \right)}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_spring_force.jpg b/doc/doc2/Eqs/fix_ti_spring_force.jpg
deleted file mode 100644
index 347102b3e7..0000000000
Binary files a/doc/doc2/Eqs/fix_ti_spring_force.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ti_spring_force.tex b/doc/doc2/Eqs/fix_ti_spring_force.tex
deleted file mode 100644
index 0acd0e54ae..0000000000
--- a/doc/doc2/Eqs/fix_ti_spring_force.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
- F_{\text{total}} = \left( 1-\lambda \right) F_{\text{solid}} + \lambda F_{\text{harm}}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_spring_function_1.jpg b/doc/doc2/Eqs/fix_ti_spring_function_1.jpg
deleted file mode 100644
index 8d3c9a78e3..0000000000
Binary files a/doc/doc2/Eqs/fix_ti_spring_function_1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ti_spring_function_1.tex b/doc/doc2/Eqs/fix_ti_spring_function_1.tex
deleted file mode 100644
index 0673410b00..0000000000
--- a/doc/doc2/Eqs/fix_ti_spring_function_1.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- \lambda(\tau) = \tau
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_ti_spring_function_2.jpg b/doc/doc2/Eqs/fix_ti_spring_function_2.jpg
deleted file mode 100644
index 96a17e63e6..0000000000
Binary files a/doc/doc2/Eqs/fix_ti_spring_function_2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ti_spring_function_2.tex b/doc/doc2/Eqs/fix_ti_spring_function_2.tex
deleted file mode 100644
index f2cb51e47d..0000000000
--- a/doc/doc2/Eqs/fix_ti_spring_function_2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- \lambda(\tau) = \tau^5 \left( 70 \tau^4 - 315 \tau^3 + 540 \tau^2 - 420 \tau + 126 \right)
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_ttm.jpg b/doc/doc2/Eqs/fix_ttm.jpg
deleted file mode 100644
index 8d9fac3fed..0000000000
Binary files a/doc/doc2/Eqs/fix_ttm.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ttm.tex b/doc/doc2/Eqs/fix_ttm.tex
deleted file mode 100644
index d5a3238f82..0000000000
--- a/doc/doc2/Eqs/fix_ttm.tex
+++ /dev/null
@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- C_e \rho_e \frac{\partial T_e}{\partial t} =
- \bigtriangledown (\kappa_e \bigtriangledown T_e) -
- g_p (T_e - T_a) + g_s T_a'
-$$
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_ttm_blast.jpg b/doc/doc2/Eqs/fix_ttm_blast.jpg
deleted file mode 100644
index d4ffe05f12..0000000000
Binary files a/doc/doc2/Eqs/fix_ttm_blast.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ttm_blast.tex b/doc/doc2/Eqs/fix_ttm_blast.tex
deleted file mode 100644
index 6871ed5cc6..0000000000
--- a/doc/doc2/Eqs/fix_ttm_blast.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- {\vec F}_i = - \partial U / \partial {\vec r}_i + {\vec F}_{langevin} - \nabla P_e/n_{ion}
-$$
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_ttm_blast1.jpg b/doc/doc2/Eqs/fix_ttm_blast1.jpg
deleted file mode 100644
index 1106c627cb..0000000000
Binary files a/doc/doc2/Eqs/fix_ttm_blast1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ttm_blast1.tex b/doc/doc2/Eqs/fix_ttm_blast1.tex
deleted file mode 100644
index 642afe4300..0000000000
--- a/doc/doc2/Eqs/fix_ttm_blast1.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- \nabla_x P_e = \left[\frac{C_e{}T_e(x)\lambda}{(x+\lambda)^2} + \frac{x}{x+\lambda}\frac{(C_e{}T_e)_{x+\Delta x}-(C_e{}T_e)_{x}}{\Delta x} \right]
-$$
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_ttm_ce.jpg b/doc/doc2/Eqs/fix_ttm_ce.jpg
deleted file mode 100644
index 4f439e31e6..0000000000
Binary files a/doc/doc2/Eqs/fix_ttm_ce.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ttm_ce.tex b/doc/doc2/Eqs/fix_ttm_ce.tex
deleted file mode 100644
index f787590b8f..0000000000
--- a/doc/doc2/Eqs/fix_ttm_ce.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- C_e = C_0 + (a_0 + a_1 X + a_2 X^2 + a_3 X^3 + a_4 X^4) \exp (-(AX)^2)
-$$
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_ttm_mod.jpg b/doc/doc2/Eqs/fix_ttm_mod.jpg
deleted file mode 100644
index 7cc67200f9..0000000000
Binary files a/doc/doc2/Eqs/fix_ttm_mod.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_ttm_mod.tex b/doc/doc2/Eqs/fix_ttm_mod.tex
deleted file mode 100644
index d0a313e676..0000000000
--- a/doc/doc2/Eqs/fix_ttm_mod.tex
+++ /dev/null
@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- C_e \rho_e \frac{\partial T_e}{\partial t} =
- \bigtriangledown (\kappa_e \bigtriangledown T_e) -
- g_p (T_e - T_a) + g_s T_a' + \theta (x-x_{surface})I_0 \exp(-x/l_{skin})
-$$
-
-\end{document}
-
-
-
-
diff --git a/doc/doc2/Eqs/fix_wall_colloid.jpg b/doc/doc2/Eqs/fix_wall_colloid.jpg
deleted file mode 100644
index 8168d3a792..0000000000
Binary files a/doc/doc2/Eqs/fix_wall_colloid.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_wall_colloid.tex b/doc/doc2/Eqs/fix_wall_colloid.tex
deleted file mode 100644
index 3ed716c263..0000000000
--- a/doc/doc2/Eqs/fix_wall_colloid.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray}
-E &=& \epsilon \left[ \frac{\sigma^{6}}{7560}
- \left(\frac{6R-D}{D^{7}} + \frac{D+8R}{(D+2R)^{7}} \right) -
- \frac{}{} \right. \nonumber \\
- &&\qquad \left. \frac{1}{6} \left(\frac{2R(D+R) + D(D+2R)
- \left[ \ln D - \ln (D+2R) \right]}{D(D+2R)} \right) \right]
-\qquad r < r_c \nonumber
-\end{eqnarray}
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_wall_harmonic.jpg b/doc/doc2/Eqs/fix_wall_harmonic.jpg
deleted file mode 100644
index 3c605690c3..0000000000
Binary files a/doc/doc2/Eqs/fix_wall_harmonic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_wall_harmonic.tex b/doc/doc2/Eqs/fix_wall_harmonic.tex
deleted file mode 100644
index 86dcb80a0e..0000000000
--- a/doc/doc2/Eqs/fix_wall_harmonic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = \epsilon \hspace{0.1cm} (r - r_c)^2 \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fix_wall_lj1043.jpg b/doc/doc2/Eqs/fix_wall_lj1043.jpg
deleted file mode 100644
index 303743bf3e..0000000000
Binary files a/doc/doc2/Eqs/fix_wall_lj1043.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_wall_lj1043.tex b/doc/doc2/Eqs/fix_wall_lj1043.tex
deleted file mode 100644
index 8ef981ca97..0000000000
--- a/doc/doc2/Eqs/fix_wall_lj1043.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = 2 \pi \epsilon \left[ \frac{2}{5} \left(\frac{\sigma}{r}\right)^{10} -
- \left(\frac{\sigma}{r}\right)^4 -
- \frac{\sqrt(2)\sigma^3}{3\left(r+\left(0.61/\sqrt(2)\right)\sigma\right)^3}\right]
- \qquad r < r_c
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/fix_wall_lj93.jpg b/doc/doc2/Eqs/fix_wall_lj93.jpg
deleted file mode 100644
index 18e502cfbf..0000000000
Binary files a/doc/doc2/Eqs/fix_wall_lj93.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fix_wall_lj93.tex b/doc/doc2/Eqs/fix_wall_lj93.tex
deleted file mode 100644
index 7372e55c15..0000000000
--- a/doc/doc2/Eqs/fix_wall_lj93.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = \epsilon \left[ \frac{2}{15} \left(\frac{\sigma}{r}\right)^{9} -
- \left(\frac{\sigma}{r}\right)^3 \right]
- \qquad r < r_c
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/fld.jpg b/doc/doc2/Eqs/fld.jpg
deleted file mode 100644
index 3d80d436ff..0000000000
Binary files a/doc/doc2/Eqs/fld.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fld.tex b/doc/doc2/Eqs/fld.tex
deleted file mode 100644
index 7c75cfbe60..0000000000
--- a/doc/doc2/Eqs/fld.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-F^{H} = -R_{FU}(U-U^{\infty}) + R_{FE}E^{\infty}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/fld2.jpg b/doc/doc2/Eqs/fld2.jpg
deleted file mode 100644
index 42de943c90..0000000000
Binary files a/doc/doc2/Eqs/fld2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/fld2.tex b/doc/doc2/Eqs/fld2.tex
deleted file mode 100644
index 43adae11db..0000000000
--- a/doc/doc2/Eqs/fld2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
--R_{FU}(U-U^{\infty}) = -R_{FE}E^{\infty} - F^{rest}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/heat_flux_J.jpg b/doc/doc2/Eqs/heat_flux_J.jpg
deleted file mode 100644
index cf3e220caa..0000000000
Binary files a/doc/doc2/Eqs/heat_flux_J.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/heat_flux_J.tex b/doc/doc2/Eqs/heat_flux_J.tex
deleted file mode 100644
index 53c0ff494a..0000000000
--- a/doc/doc2/Eqs/heat_flux_J.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\mathbf{J} & = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i - \sum_{i} \mathbf{S}_{i} \mathbf{v}_i \right] \\
-& = & \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \sum_{i r_{\rm out} \\
- E & = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\
- & = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
- & = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\
- LJ(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^6 \right] \\
- C(r) & = & \frac{C q_i q_j}{ \epsilon r} \\
- S(r) & = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
- \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
- { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
-\end{eqnarray*}
-
-\end{document}
-
-
diff --git a/doc/doc2/Eqs/pair_class2.jpg b/doc/doc2/Eqs/pair_class2.jpg
deleted file mode 100644
index abec072e79..0000000000
Binary files a/doc/doc2/Eqs/pair_class2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_class2.tex b/doc/doc2/Eqs/pair_class2.tex
deleted file mode 100644
index e2acc00bb6..0000000000
--- a/doc/doc2/Eqs/pair_class2.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 -
- 3 \left(\frac{\sigma}{r}\right)^6 \right]
- \qquad r < r_c
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_cmm.jpg b/doc/doc2/Eqs/pair_cmm.jpg
deleted file mode 100644
index 1ec60f7305..0000000000
Binary files a/doc/doc2/Eqs/pair_cmm.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_cmm.tex b/doc/doc2/Eqs/pair_cmm.tex
deleted file mode 100644
index 9bab1e9002..0000000000
--- a/doc/doc2/Eqs/pair_cmm.tex
+++ /dev/null
@@ -1,16 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E = & \frac{27}{4} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} -
- \left(\frac{\sigma}{r}\right)^6 \right] &
- \qquad r < r_c \\
- E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^4 \right] &
- \qquad r < r_c \\
- E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^6 \right] &
- \qquad r < r_c
-\end{eqnarray*}
-\end{document}
diff --git a/doc/doc2/Eqs/pair_colloid_cc.jpg b/doc/doc2/Eqs/pair_colloid_cc.jpg
deleted file mode 100644
index a64094ddad..0000000000
Binary files a/doc/doc2/Eqs/pair_colloid_cc.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_colloid_cc.tex b/doc/doc2/Eqs/pair_colloid_cc.tex
deleted file mode 100644
index e1485d325a..0000000000
--- a/doc/doc2/Eqs/pair_colloid_cc.tex
+++ /dev/null
@@ -1,31 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray}
-U_A &=& - \frac{A_{cc}}{6} \left[
- \frac{2 a_1 a_2}{r^2-\left(a_1+a_2\right)^2}
- + \frac{2 a_1 a_2}{r^2 - \left(a_1 - a_2\right)^2}
- + \mathrm{ln}
- \left(
- \frac{r^2-\left(a_1+a_2\right)^2}{r^2-\left(a_1-a_2\right)^2}
- \right)
- \right] \nonumber \\
-\nonumber \\
-U_R &=& \frac{A_{cc}}{37800} \frac{\sigma^6}{r}
-\left[ \frac{}{} \right. \nonumber \\
- &&\qquad \frac{r^2-7r\left(a_1+a_2\right)+6\left(a_1^2+7a_1a_2+a_2^2\right)}
- {\left(r-a_1-a_2\right)^7} \nonumber \\
- &&\qquad +\frac{r^2+7r\left(a_1+a_2\right)+6\left(a_1^2+7a_1a_2+a_2^2\right)}
- {\left(r+a_1+a_2\right)^7} \nonumber \\
- &&\qquad -\frac{r^2+7r\left(a_1-a_2\right)+6\left(a_1^2-7a_1a_2+a_2^2\right)}
- {\left(r+a_1-a_2\right)^7} \nonumber \\
- &&\qquad \left. -\frac{r^2-7r\left(a_1-a_2\right)+6\left(a_1^2-7a_1a_2+a_2^2\right)}
- {\left(r-a_1+a_2\right)^7}
- \right] \nonumber \\
-\nonumber \\
-U &=& U_A + U_R, \qquad r < r_c \nonumber
-\end{eqnarray}
-
-\end{document}
-
diff --git a/doc/doc2/Eqs/pair_colloid_cs.jpg b/doc/doc2/Eqs/pair_colloid_cs.jpg
deleted file mode 100644
index 8f5948fa54..0000000000
Binary files a/doc/doc2/Eqs/pair_colloid_cs.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_colloid_cs.tex b/doc/doc2/Eqs/pair_colloid_cs.tex
deleted file mode 100644
index 760215ee08..0000000000
--- a/doc/doc2/Eqs/pair_colloid_cs.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray}
- U &=& \frac{2 ~ a^3 ~ \sigma^3 ~ A_{cs}}{9 \left( a^2 - r^2 \right)^3}
- \left[ 1 - \frac{\left(5 ~ a^6+45~a^4~r^2+63~a^2~r^4+15~r^6\right) \sigma^6}
- {15 \left(a-r\right)^6 \left( a+r \right)^6} \right], ~~ r < r_c \nonumber
-\end{eqnarray}
-
-\end{document}
-
diff --git a/doc/doc2/Eqs/pair_colloid_ss.jpg b/doc/doc2/Eqs/pair_colloid_ss.jpg
deleted file mode 100644
index 4ce19ba1e8..0000000000
Binary files a/doc/doc2/Eqs/pair_colloid_ss.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_colloid_ss.tex b/doc/doc2/Eqs/pair_colloid_ss.tex
deleted file mode 100644
index 1cc511ed06..0000000000
--- a/doc/doc2/Eqs/pair_colloid_ss.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray}
- U &=& \frac{A_{ss}}{36} \left[ \left( \frac{\sigma}{r}
- \right)^{12} - \left( \frac{ \sigma}{r} \right)^6 \right], ~~
- r < r_c \nonumber
-\end{eqnarray}
-
-\end{document}
-
diff --git a/doc/doc2/Eqs/pair_comb1.jpg b/doc/doc2/Eqs/pair_comb1.jpg
deleted file mode 100644
index e0711ca972..0000000000
Binary files a/doc/doc2/Eqs/pair_comb1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_comb1.tex b/doc/doc2/Eqs/pair_comb1.tex
deleted file mode 100644
index aab7c8d2d4..0000000000
--- a/doc/doc2/Eqs/pair_comb1.tex
+++ /dev/null
@@ -1,7 +0,0 @@
-\documentclass[12pt]{article}
-\begin{document} \large
-\begin{eqnarray*}
-E_T & = & \sum_i [ E_i^{self} (q_i) + \sum_{j>i} [E_{ij}^{short} (r_{ij}, q_i, q_j) + E_{ij}^{Coul} (r_{ij}, q_i, q_j)] + \\
-&& E^{polar} (q_i, r_{ij}) + E^{vdW} (r_{ij}) + E^{barr} (q_i) + E^{corr} (r_{ij}, \theta_{jik})] \\
-\end{eqnarray*}
-\end{document}
diff --git a/doc/doc2/Eqs/pair_comb2.jpg b/doc/doc2/Eqs/pair_comb2.jpg
deleted file mode 100644
index 8b0e5ba51a..0000000000
Binary files a/doc/doc2/Eqs/pair_comb2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_comb2.tex b/doc/doc2/Eqs/pair_comb2.tex
deleted file mode 100644
index cd022cc7f4..0000000000
--- a/doc/doc2/Eqs/pair_comb2.tex
+++ /dev/null
@@ -1,23 +0,0 @@
-\documentclass[10pt]{article}
-
-\begin{document}
-
-\begin{table}[h]
-\begin{tabular}{|c|c|c|c|c|c|c|c|c|}
-\hline
- & $O$ & $Cu$ & $N$ & $C$ & $H$ & $Ti$ & $Zn$ & $Zr$ \\ \hline
-$O$ & F & F & F & F & F & F & F & F\\ \hline
-$Cu$ & F & F & P & F & F & P & F & P \\ \hline
-$N$ & F & P & F & M & F & P & P & P \\ \hline
-$C$ & F & F & M & F & F & M & M & M \\ \hline
-$H$ & F & F & F & F & F & M & M & F \\ \hline
-$Ti$ & F & P & P & M & M & F & P & P \\ \hline
-$Zn$ & F & F & P & M & M & P & F & P \\ \hline
-$Zr$ & F & P & P & M & F & P & P & F \\ \hline
-\multicolumn{9}{l}{F: Fully optimized} \\
-\multicolumn{9}{l}{M: Only optimized for dimer molecule} \\
-\multicolumn{9}{l}{P: in Progress but have it from mixing rule} \\
-\end{tabular}
-\end{table}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_coul_diel.jpg b/doc/doc2/Eqs/pair_coul_diel.jpg
deleted file mode 100644
index 70cb84f7a5..0000000000
Binary files a/doc/doc2/Eqs/pair_coul_diel.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_coul_diel.tex b/doc/doc2/Eqs/pair_coul_diel.tex
deleted file mode 100644
index f0b893d887..0000000000
--- a/doc/doc2/Eqs/pair_coul_diel.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
- E & = & \frac{Cq_iq_j}{\epsilon r} \left( \frac{\epsilon}{\epsilon_D(r)}-1\right) \qquad r < r_c \\
- \epsilon_D(r) & = & \frac{5.2+\epsilon}{2} + \frac{\epsilon-5.2}{2}\tanh\left(\frac{r-r_{me}}{\sigma_e}\right)
-\end{eqnarray*}
-\end{document}
diff --git a/doc/doc2/Eqs/pair_coul_dsf.jpg b/doc/doc2/Eqs/pair_coul_dsf.jpg
deleted file mode 100644
index a891b3ad15..0000000000
Binary files a/doc/doc2/Eqs/pair_coul_dsf.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_coul_dsf.tex b/doc/doc2/Eqs/pair_coul_dsf.tex
deleted file mode 100644
index ec69680fc8..0000000000
--- a/doc/doc2/Eqs/pair_coul_dsf.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-$$
- E =
- q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} +
- \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_coul_soft.jpg b/doc/doc2/Eqs/pair_coul_soft.jpg
deleted file mode 100644
index dad9c745ba..0000000000
Binary files a/doc/doc2/Eqs/pair_coul_soft.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_coul_soft.tex b/doc/doc2/Eqs/pair_coul_soft.tex
deleted file mode 100644
index 2ff42a25b6..0000000000
--- a/doc/doc2/Eqs/pair_coul_soft.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[
-E = \lambda^n \frac{ C q_i q_j}{\epsilon
-\left[ \alpha_{\mathrm{C}} (1-\lambda)^2 + r^2 \right]^{1/2}} \qquad r < r_c
-\]
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_coul_wolf.jpg b/doc/doc2/Eqs/pair_coul_wolf.jpg
deleted file mode 100644
index fd64cb6c03..0000000000
Binary files a/doc/doc2/Eqs/pair_coul_wolf.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_coul_wolf.tex b/doc/doc2/Eqs/pair_coul_wolf.tex
deleted file mode 100644
index 4a6592638f..0000000000
--- a/doc/doc2/Eqs/pair_coul_wolf.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-$$
- E_i = \frac{1}{2} \sum_{j \neq i}
- \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
- \frac{1}{2} \sum_{j \neq i}
- \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_coulomb.jpg b/doc/doc2/Eqs/pair_coulomb.jpg
deleted file mode 100644
index 39aaebac31..0000000000
Binary files a/doc/doc2/Eqs/pair_coulomb.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_coulomb.tex b/doc/doc2/Eqs/pair_coulomb.tex
deleted file mode 100644
index 9dacdc1af3..0000000000
--- a/doc/doc2/Eqs/pair_coulomb.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_cs.jpg b/doc/doc2/Eqs/pair_cs.jpg
deleted file mode 100644
index b870a3bdf4..0000000000
Binary files a/doc/doc2/Eqs/pair_cs.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_cs.tex b/doc/doc2/Eqs/pair_cs.tex
deleted file mode 100644
index b7eacb8d5b..0000000000
--- a/doc/doc2/Eqs/pair_cs.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = \frac{C q_i q_j}{\epsilon (r + r_{min})} \qquad r \rightarrow 0
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_debye.jpg b/doc/doc2/Eqs/pair_debye.jpg
deleted file mode 100644
index 42bcb5cc63..0000000000
Binary files a/doc/doc2/Eqs/pair_debye.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_debye.tex b/doc/doc2/Eqs/pair_debye.tex
deleted file mode 100644
index 392a6516ce..0000000000
--- a/doc/doc2/Eqs/pair_debye.tex
+++ /dev/null
@@ -1,8 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-$$
- E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_dipole.jpg b/doc/doc2/Eqs/pair_dipole.jpg
deleted file mode 100644
index e106c17c91..0000000000
Binary files a/doc/doc2/Eqs/pair_dipole.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_dipole.tex b/doc/doc2/Eqs/pair_dipole.tex
deleted file mode 100644
index bc0ae82f80..0000000000
--- a/doc/doc2/Eqs/pair_dipole.tex
+++ /dev/null
@@ -1,38 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-E_{LJ} & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^6 \right] \\
-E_{qq} & = & \frac{q_i q_j}{r} \\
-E_{qp} & = & \frac{q}{r^3} (p \bullet \vec{r}) \\
-E_{pp} & = & \frac{1}{r^3} (\vec{p_i} \bullet \vec{p_j}) -
- \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})
-\end{eqnarray*}
-
-\begin{eqnarray*}
-F_{qq} & = & \frac{q_i q_j}{r^3} \vec{r} \\
-F_{qp} & = & -\frac{q}{r^3} \vec{p} + \frac{3q}{r^5}
- (\vec{p} \bullet \vec{r}) \vec{r} \\
-F_{pp} & = & \frac{3}{r^5} (\vec{p_i} \bullet \vec{p_j}) \vec{r} -
- \frac{15}{r^7} (\vec{p_i} \bullet \vec{r})
- (\vec{p_j} \bullet \vec{r}) \vec{r} +
- \frac{3}{r^5} \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} +
- (\vec{p_i} \bullet \vec{r}) \vec{p_j} \right]
-\end{eqnarray*}
-
-\begin{eqnarray*}
-T_{pq} = T_{ij} & = & \frac{q_j}{r^3} (\vec{p_i} \times \vec{r}) \\
-T_{qp} = T_{ji} & = & - \frac{q_i}{r^3} (\vec{p_j} \times \vec{r}) \\
-T_{pp} = T_{ij} & = & -\frac{1}{r^3} (\vec{p_i} \times \vec{p_j}) +
- \frac{3}{r^5} (\vec{p_j} \bullet \vec{r})
- (\vec{p_i} \times \vec{r}) \\
-T_{pp} = T_{ji} & = & -\frac{1}{r^3} (\vec{p_j} \times \vec{p_i}) +
- \frac{3}{r^5} (\vec{p_i} \bullet \vec{r})
- (\vec{p_j} \times \vec{r}) \\
-\end{eqnarray*}
-
-\end{document}
-
-
diff --git a/doc/doc2/Eqs/pair_dipole_sf.jpg b/doc/doc2/Eqs/pair_dipole_sf.jpg
deleted file mode 100644
index c591534550..0000000000
Binary files a/doc/doc2/Eqs/pair_dipole_sf.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_dipole_sf.tex b/doc/doc2/Eqs/pair_dipole_sf.tex
deleted file mode 100644
index c653a37740..0000000000
--- a/doc/doc2/Eqs/pair_dipole_sf.tex
+++ /dev/null
@@ -1,51 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-E_{LJ} & = & 4\epsilon \left\{ \left[ \left( \frac{\sigma}{r} \right)^{\!12} -
- \left( \frac{\sigma}{r} \right)^{\!6} \right] +
- \left[ 6\left( \frac{\sigma}{r_c} \right)^{\!12} -
- 3\left(\frac{\sigma}{r_c}\right)^{\!6}\right]\left(\frac{r}{r_c}\right)^{\!2}
- - 7\left( \frac{\sigma}{r_c} \right)^{\!12} +
- 4\left( \frac{\sigma}{r_c} \right)^{\!6}\right\} \\
-E_{qq} & = & \frac{q_i q_j}{r}\left(1-\frac{r}{r_c}\right)^{\!2} \\
-E_{pq} & = & E_{ji} = -\frac{q}{r^3} \left[ 1 -
- 3\left(\frac{r}{r_c}\right)^{\!2} +
- 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\
-E_{qp} & = & E_{ij} = \frac{q}{r^3} \left[ 1 -
- 3\left(\frac{r}{r_c}\right)^{\!2} +
- 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\
-E_{pp} & = & \left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
- 3\left(\frac{r}{r_c}\right)^{\!4}\right]\left[\frac{1}{r^3}
- (\vec{p_i} \bullet \vec{p_j}) - \frac{3}{r^5}
- (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})\right] \\
-\end{eqnarray*}
-
-\begin{eqnarray*}
-F_{LJ} & = & \left\{\left[48\epsilon \left(\frac{\sigma}{r}\right)^{\!12} -
- 24\epsilon \left(\frac{\sigma}{r}\right)^{\!6} \right]\frac{1}{r^2} -
- \left[48\epsilon \left(\frac{\sigma}{r_c}\right)^{\!12} - 24\epsilon
- \left(\frac{\sigma}{r_c}\right)^{\!6} \right]\frac{1}{r_c^2}\right\}\vec{r}\\
-F_{qq} & = & \frac{q_i q_j}{r}\left(\frac{1}{r^2} -
- \frac{1}{r_c^2}\right)\vec{r} \\
-F_{pq} &=& F_{ij } = -\frac{3q}{r^5} \left[ 1 -
- \left(\frac{r}{r_c}\right)^{\!2}\right](\vec{p}\bullet\vec{r})\vec{r} +
- \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} +
- 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\
-F_{qp} &=& F_{ij} = \frac{3q}{r^5} \left[ 1 -
- \left(\frac{r}{r_c}\right)^{\!2}\right] (\vec{p}\bullet\vec{r})\vec{r} -
- \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} +
- 2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\
-F_{pp} & = &\frac{3}{r^5}\Bigg\{\left[1-\left(\frac{r}{r_c}\right)^{\!4}\right]
- \left[(\vec{p_i}\bullet\vec{p_j}) - \frac{3}{r^2} (\vec{p_i}\bullet\vec{r})
- (\vec{p_j} \bullet \vec{r})\right] \vec{r} + \\
- & & \left[1 -
- 4\left(\frac{r}{r_c}\right)^{\!3}+3\left(\frac{r}{r_c}\right)^{\!4}\right]
- \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + (\vec{p_i} \bullet \vec{r})
- \vec{p_j} -\frac{2}{r^2} (\vec{p_i} \bullet \vec{r})
- (\vec{p_j} \bullet \vec{r})\vec{r}\right] \Bigg\} \\
-\end{eqnarray*}
-
-\end{document}
-
diff --git a/doc/doc2/Eqs/pair_dipole_sf2.jpg b/doc/doc2/Eqs/pair_dipole_sf2.jpg
deleted file mode 100644
index b9e57becf6..0000000000
Binary files a/doc/doc2/Eqs/pair_dipole_sf2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_dipole_sf2.tex b/doc/doc2/Eqs/pair_dipole_sf2.tex
deleted file mode 100644
index 74758ba230..0000000000
--- a/doc/doc2/Eqs/pair_dipole_sf2.tex
+++ /dev/null
@@ -1,24 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-T_{pq} = T_{ij} & = & \frac{q_j}{r^3} \left[ 1 -
- 3\left(\frac{r}{r_c}\right)^{\!2} +
- 2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p_i}\times\vec{r}) \\
-T_{qp} = T_{ji} & = & - \frac{q_i}{r^3} \left[ 1 -
- 3\left(\frac{r}{r_c}\right)^{\!2} +
- 2\left(\frac{r}{r_c}\right)^{\!3} \right] (\vec{p_j}\times\vec{r}) \\
-T_{pp} = T_{ij} & = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
- e3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \times \vec{p_j}) + \\
- & & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
- 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_j}\bullet\vec{r})
- (\vec{p_i} \times \vec{r}) \\
-T_{pp} = T_{ji} & = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
- 3\left(\frac{r}{r_c}\right)^{\!4}\right](\vec{p_j} \times \vec{p_i}) + \\
- & & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
- 3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \bullet \vec{r})
- (\vec{p_j} \times \vec{r}) \\
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_dpd.jpg b/doc/doc2/Eqs/pair_dpd.jpg
deleted file mode 100644
index e9bb8a69af..0000000000
Binary files a/doc/doc2/Eqs/pair_dpd.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_dpd.tex b/doc/doc2/Eqs/pair_dpd.tex
deleted file mode 100644
index ba47f0d6b6..0000000000
--- a/doc/doc2/Eqs/pair_dpd.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- \vec{f} & = & (F^C + F^D + F^R) \hat{r_{ij}} \qquad \qquad r < r_c \\
- F^C & = & A w(r) \\
- F^D & = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v_{ij}}) \\
- F^R & = & \sigma w(r) \alpha (\Delta t)^{-1/2} \\
- w(r) & = & 1 - r/r_c
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_eam.jpg b/doc/doc2/Eqs/pair_eam.jpg
deleted file mode 100644
index 95c86b4ced..0000000000
Binary files a/doc/doc2/Eqs/pair_eam.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_eam.tex b/doc/doc2/Eqs/pair_eam.tex
deleted file mode 100644
index 2ea20b2198..0000000000
--- a/doc/doc2/Eqs/pair_eam.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E_i = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) +
- \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_eam_fs.jpg b/doc/doc2/Eqs/pair_eam_fs.jpg
deleted file mode 100644
index fa72f8fc73..0000000000
Binary files a/doc/doc2/Eqs/pair_eam_fs.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_eam_fs.tex b/doc/doc2/Eqs/pair_eam_fs.tex
deleted file mode 100644
index 32ca605e2e..0000000000
--- a/doc/doc2/Eqs/pair_eam_fs.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E_i = F_\alpha \left(\sum_{j \neq i}\
- \rho_{\alpha\beta} (r_{ij})\right) +
- \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_edip.jpg b/doc/doc2/Eqs/pair_edip.jpg
deleted file mode 100644
index 3933280480..0000000000
Binary files a/doc/doc2/Eqs/pair_edip.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_edip.tex b/doc/doc2/Eqs/pair_edip.tex
deleted file mode 100644
index 27f5dd9eec..0000000000
--- a/doc/doc2/Eqs/pair_edip.tex
+++ /dev/null
@@ -1,22 +0,0 @@
-\documentclass[12pt]{article}
-
-\usepackage{amssymb,amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
-E & = & \sum_{j \ne i} \phi_{2}(R_{ij}, Z_{i}) + \sum_{j \ne i} \sum_{k \ne i,k > j} \phi_{3}(R_{ij}, R_{ik}, Z_{i}) \\
-\phi_{2}(r, Z) & = & A\left[\left(\frac{B}{r}\right)^{\rho} - e^{-\beta Z^2}\right]exp{\left(\frac{\sigma}{r-a}\right)} \\
-\phi_{3}(R_{ij}, R_{ik}, Z_i) & = & exp{\left(\frac{\gamma}{R_{ij}-a}\right)}exp{\left(\frac{\gamma}{R_{ik}-a}\right)}h(cos\theta_{ijk},Z_i) \\
-Z_i & = & \sum_{m \ne i} f(R_{im}) \qquad
- f(r) = \begin{cases}
- 1 & \quad ra
- \end{cases} \\
-h(l,Z) & = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\
-Q(Z) & = & Q_0 e^{-\mu Z} \qquad \tau(Z) = u_1 + u_2 (u_3 e^{-u_4 Z} - e^{-2u_4 Z})
-\end{eqnarray*}
-
-\end{document}
-
diff --git a/doc/doc2/Eqs/pair_eim1.jpg b/doc/doc2/Eqs/pair_eim1.jpg
deleted file mode 100644
index c243120b2a..0000000000
Binary files a/doc/doc2/Eqs/pair_eim1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_eim1.tex b/doc/doc2/Eqs/pair_eim1.tex
deleted file mode 100644
index bfa5b6ebc4..0000000000
--- a/doc/doc2/Eqs/pair_eim1.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E = \frac{1}{2} \sum_{i=1}^{N} \sum_{j=i_1}^{i_N} \phi_{ij} \left(r_{ij}\right) + \sum_{i=1}^{N}E_i\left(q_i,\sigma_i\right)
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_eim2.jpg b/doc/doc2/Eqs/pair_eim2.jpg
deleted file mode 100644
index 4896f658f1..0000000000
Binary files a/doc/doc2/Eqs/pair_eim2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_eim2.tex b/doc/doc2/Eqs/pair_eim2.tex
deleted file mode 100644
index d8c4181342..0000000000
--- a/doc/doc2/Eqs/pair_eim2.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-q_i & = & \sum_{j=i_1}^{i_N} \eta_{ji}\left(r_{ij}\right) \\
-\sigma_i & = & \sum_{j=i_1}^{i_N} q_j \cdot \psi_{ij} \left(r_{ij}\right) \\
-E_i\left(q_i,\sigma_i\right) & = & \frac{1}{2} \cdot q_i \cdot \sigma_i
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_eim3.jpg b/doc/doc2/Eqs/pair_eim3.jpg
deleted file mode 100644
index 57366bc15d..0000000000
Binary files a/doc/doc2/Eqs/pair_eim3.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_eim3.tex b/doc/doc2/Eqs/pair_eim3.tex
deleted file mode 100644
index 84343c6acf..0000000000
--- a/doc/doc2/Eqs/pair_eim3.tex
+++ /dev/null
@@ -1,25 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\phi_{ij}\left(r\right) = \left\{ \begin{array}{lr}
-\left[\frac{E_{b,ij}\beta_{ij}}{\beta_{ij}-\alpha_{ij}}\exp\left(-\alpha_{ij} \frac{r-r_{e,ij}}{r_{e,ij}}\right)-\frac{E_{b,ij}\alpha_{ij}}{\beta_{ij}-\alpha_{ij}}\exp\left(-\beta_{ij} \frac{r-r_{e,ij}}{r_{e,ij}}\right)\right]f_c\left(r,r_{e,ij},r_{c,\phi,ij}\right),& p_{ij}=1 \\
-\left[\frac{E_{b,ij}\beta_{ij}}{\beta_{ij}-\alpha_{ij}} \left(\frac{r_{e,ij}}{r}\right)^{\alpha_{ij}} -\frac{E_{b,ij}\alpha_{ij}}{\beta_{ij}-\alpha_{ij}} \left(\frac{r_{e,ij}}{r}\right)^{\beta_{ij}}\right]f_c\left(r,r_{e,ij},r_{c,\phi,ij}\right),& p_{ij}=2
-\end{array}
-\right.
-\end{eqnarray*}
-
-$$
-\eta_{ji} = A_{\eta,ij}\left(\chi_j-\chi_i\right)f_c\left(r,r_{s,\eta,ij},r_{c,\eta,ij}\right)
-$$
-
-$$
-\psi_{ij}\left(r\right) = A_{\psi,ij}\exp\left(-\zeta_{ij}r\right)f_c\left(r,r_{s,\psi,ij},r_{c,\psi,ij}\right)
-$$
-
-$$
-f_{c}\left(r,r_p,r_c\right) = 0.510204 erfc\left[\frac{1.64498\left(2r-r_p-r_c\right)}{r_c-r_p}\right] - 0.010204
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_gauss.jpg b/doc/doc2/Eqs/pair_gauss.jpg
deleted file mode 100644
index 97c2f0ecb2..0000000000
Binary files a/doc/doc2/Eqs/pair_gauss.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_gauss.tex b/doc/doc2/Eqs/pair_gauss.tex
deleted file mode 100644
index ed38e13943..0000000000
--- a/doc/doc2/Eqs/pair_gauss.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-$$
- E = - A \exp(-B r^2) \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_gauss_cut.jpg b/doc/doc2/Eqs/pair_gauss_cut.jpg
deleted file mode 100644
index e47bb8cc06..0000000000
Binary files a/doc/doc2/Eqs/pair_gauss_cut.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_gauss_cut.tex b/doc/doc2/Eqs/pair_gauss_cut.tex
deleted file mode 100644
index 5d0bb430f3..0000000000
--- a/doc/doc2/Eqs/pair_gauss_cut.tex
+++ /dev/null
@@ -1,8 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
- E = & \frac{H}{\sigma_h\sqrt{2\pi}} \exp\left[-\frac{(r-r_{mh})^2}{2\sigma_h^2}\right]
-\end{eqnarray*}
-\end{document}
diff --git a/doc/doc2/Eqs/pair_gayberne.jpg b/doc/doc2/Eqs/pair_gayberne.jpg
deleted file mode 100644
index e9b1f3ca93..0000000000
Binary files a/doc/doc2/Eqs/pair_gayberne.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_gayberne.tex b/doc/doc2/Eqs/pair_gayberne.tex
deleted file mode 100644
index d3c199e826..0000000000
--- a/doc/doc2/Eqs/pair_gayberne.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ U ( \mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12} ) = U_r (
-\mathbf{A}_1, \mathbf{A}_2, \mathbf{r}_{12}, \gamma ) \cdot \eta_{12} (
-\mathbf{A}_1, \mathbf{A}_2, \upsilon ) \cdot \chi_{12} ( \mathbf{A}_1,
-\mathbf{A}_2, \mathbf{r}_{12}, \mu ) $$
-
-$$ U_r = 4 \epsilon ( \varrho^{12} - \varrho^6) $$
-
-$$ \varrho = \frac{\sigma}{ h_{12} + \gamma \sigma} $$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_gayberne2.jpg b/doc/doc2/Eqs/pair_gayberne2.jpg
deleted file mode 100644
index a4e6c6f70f..0000000000
Binary files a/doc/doc2/Eqs/pair_gayberne2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_gayberne2.tex b/doc/doc2/Eqs/pair_gayberne2.tex
deleted file mode 100644
index 6efb755774..0000000000
--- a/doc/doc2/Eqs/pair_gayberne2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ \epsilon_a = \sigma \cdot { \frac{a}{ b \cdot c } }; \epsilon_b =
-\sigma \cdot { \frac{b}{ a \cdot c } }; \epsilon_c = \sigma \cdot {
-\frac{c}{ a \cdot b } } $$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_gran_hertz.jpg b/doc/doc2/Eqs/pair_gran_hertz.jpg
deleted file mode 100644
index 733875fee6..0000000000
Binary files a/doc/doc2/Eqs/pair_gran_hertz.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_gran_hertz.tex b/doc/doc2/Eqs/pair_gran_hertz.tex
deleted file mode 100644
index d6e09493b2..0000000000
--- a/doc/doc2/Eqs/pair_gran_hertz.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- F_{hz} = \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}} F_{hk} =
- \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}}
- \Big[ (k_n \delta \mathbf{n}_{ij} -
- m_{\mbox{\scriptsize{eff}}} \: \gamma_n \mathbf{ v}_n) -
- (k_t \mathbf{ \Delta s}_t +
- m_{\mbox{\scriptsize{eff}}} \: \gamma_t \mathbf{v}_t) \Big]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_gran_hooke.jpg b/doc/doc2/Eqs/pair_gran_hooke.jpg
deleted file mode 100644
index 36f34db6c6..0000000000
Binary files a/doc/doc2/Eqs/pair_gran_hooke.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_gran_hooke.tex b/doc/doc2/Eqs/pair_gran_hooke.tex
deleted file mode 100644
index e1901e66a3..0000000000
--- a/doc/doc2/Eqs/pair_gran_hooke.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- F_{hk} = (k_n \delta \mathbf{n}_{ij} -
- m_{\mbox{\scriptsize{eff}}} \gamma_n\mathbf{ v}_n) -
- (k_t \mathbf{ \Delta s}_t +
- m_{\mbox{\scriptsize{eff}}} \gamma_t \mathbf{v}_t)
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_gromacs.jpg b/doc/doc2/Eqs/pair_gromacs.jpg
deleted file mode 100644
index 885c059e65..0000000000
Binary files a/doc/doc2/Eqs/pair_gromacs.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_gromacs.tex b/doc/doc2/Eqs/pair_gromacs.tex
deleted file mode 100644
index 88dbe15909..0000000000
--- a/doc/doc2/Eqs/pair_gromacs.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-E_{LJ} & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^6 \right] + S_{LJ}(r)
- \qquad r < r_c \\
-E_C & = & \frac{C q_i q_j}{\epsilon r} + S_C(r) \qquad r < r_c \\
-S(r) & = & C \qquad r < r_1 \\
-S(r) & = & \frac{A}{3} (r - r_1)^3 + \frac{B}{4} (r - r_1)^4 + C \qquad r_1 < r < r_c \\
-A & = & (-3 E'(r_c) + (r_c - r_1) E''(r_c))/(r_c - r_1)^2 \\
-B & = & (2 E'(r_c) - (r_c - r_1) E''(r_c))/(r_c - r_1)^3 \\
-C & = & -E(r_c) + \frac{1}{2} (r_c - r_1) E'(r_c) - \frac{1}{12} (r_c - r_1)^2 E''(r_c)) \\
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_hbond_dreiding.jpg b/doc/doc2/Eqs/pair_hbond_dreiding.jpg
deleted file mode 100644
index b93044ed31..0000000000
Binary files a/doc/doc2/Eqs/pair_hbond_dreiding.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_hbond_dreiding.tex b/doc/doc2/Eqs/pair_hbond_dreiding.tex
deleted file mode 100644
index 9663ee5608..0000000000
--- a/doc/doc2/Eqs/pair_hbond_dreiding.tex
+++ /dev/null
@@ -1,18 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-\begin{eqnarray*}
- E & = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_{\rm in} \\
- & = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
- & = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_{\rm out} \\
- LJ(r) & = & AR^{-12}-BR^{-10}cos^n\theta=
- \epsilon\left\lbrace 5\left[ \frac{\sigma}{r}\right]^{12}-
- 6\left[ \frac{\sigma}{r}\right]^{10} \right\rbrace cos^n\theta\\
- Morse(r) & = & D_0\left\lbrace \chi^2 - 2\chi\right\rbrace cos^n\theta=
- D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)}
- \right\rbrace cos^n\theta \\
- S(r) & = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
- \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
- { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
-\end{eqnarray*}
-\end{document}
diff --git a/doc/doc2/Eqs/pair_lj.jpg b/doc/doc2/Eqs/pair_lj.jpg
deleted file mode 100644
index 49cf7f5eb9..0000000000
Binary files a/doc/doc2/Eqs/pair_lj.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_lj.tex b/doc/doc2/Eqs/pair_lj.tex
deleted file mode 100644
index 011fb8b769..0000000000
--- a/doc/doc2/Eqs/pair_lj.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^6 \right]
- \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_lj96.jpg b/doc/doc2/Eqs/pair_lj96.jpg
deleted file mode 100644
index 6462de180e..0000000000
Binary files a/doc/doc2/Eqs/pair_lj96.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_lj96.tex b/doc/doc2/Eqs/pair_lj96.tex
deleted file mode 100644
index e970624892..0000000000
--- a/doc/doc2/Eqs/pair_lj96.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{9} -
- \left(\frac{\sigma}{r}\right)^6 \right]
- \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_lj_cubic.jpg b/doc/doc2/Eqs/pair_lj_cubic.jpg
deleted file mode 100644
index 69ec4f6e84..0000000000
Binary files a/doc/doc2/Eqs/pair_lj_cubic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_lj_cubic.tex b/doc/doc2/Eqs/pair_lj_cubic.tex
deleted file mode 100644
index e2e1b67dd7..0000000000
--- a/doc/doc2/Eqs/pair_lj_cubic.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E &=& u_{LJ}(r) \qquad r \leq r_s \\
- &=& u_{LJ}(r_s) + (r-r_s) u'_{LJ}(r_s) - \frac{1}{6} A_3 (r-r_s)^3 \qquad r_s < r \leq r_c \\
- &=& 0 \qquad r > r_c
-\end{eqnarray*}
-
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_lj_expand.jpg b/doc/doc2/Eqs/pair_lj_expand.jpg
deleted file mode 100644
index e274818892..0000000000
Binary files a/doc/doc2/Eqs/pair_lj_expand.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_lj_expand.tex b/doc/doc2/Eqs/pair_lj_expand.tex
deleted file mode 100644
index 0aaa2f44d8..0000000000
--- a/doc/doc2/Eqs/pair_lj_expand.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = 4 \epsilon \left[ \left(\frac{\sigma}{r - \Delta}\right)^{12} -
- \left(\frac{\sigma}{r - \Delta}\right)^6 \right]
- \qquad r < r_c + \Delta
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_lj_sf.jpg b/doc/doc2/Eqs/pair_lj_sf.jpg
deleted file mode 100644
index a702240003..0000000000
Binary files a/doc/doc2/Eqs/pair_lj_sf.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_lj_sf.tex b/doc/doc2/Eqs/pair_lj_sf.tex
deleted file mode 100644
index e78e2ca75f..0000000000
--- a/doc/doc2/Eqs/pair_lj_sf.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
- E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\
- \mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r)
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_lj_smooth.jpg b/doc/doc2/Eqs/pair_lj_smooth.jpg
deleted file mode 100644
index d380fd345c..0000000000
Binary files a/doc/doc2/Eqs/pair_lj_smooth.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_lj_smooth.tex b/doc/doc2/Eqs/pair_lj_smooth.tex
deleted file mode 100644
index 5aa5495c27..0000000000
--- a/doc/doc2/Eqs/pair_lj_smooth.tex
+++ /dev/null
@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^6 \right]
- \qquad r < r_{in} \\
- F & = & C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3
- \qquad r_{in} < r < r_c
-\end{eqnarray*}
-
-\end{document}
-
-
diff --git a/doc/doc2/Eqs/pair_lj_smooth_linear.jpg b/doc/doc2/Eqs/pair_lj_smooth_linear.jpg
deleted file mode 100644
index b0626abae1..0000000000
Binary files a/doc/doc2/Eqs/pair_lj_smooth_linear.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_lj_smooth_linear.tex b/doc/doc2/Eqs/pair_lj_smooth_linear.tex
deleted file mode 100644
index b8980f8d25..0000000000
--- a/doc/doc2/Eqs/pair_lj_smooth_linear.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\phi\left(r\right) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
- \left(\frac{\sigma}{r}\right)^6 \right] \\
-E\left(r\right) & = & \phi\left(r\right) - \phi\left(R_c\right) - \left(r - R_c\right) \left.\frac{d\phi}{d r} \right|_{r=R_c} \qquad r < R_c
-\end{eqnarray*}
-
-\end{document}
-
-
diff --git a/doc/doc2/Eqs/pair_lj_soft.jpg b/doc/doc2/Eqs/pair_lj_soft.jpg
deleted file mode 100644
index 856d6d5bbc..0000000000
Binary files a/doc/doc2/Eqs/pair_lj_soft.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_lj_soft.tex b/doc/doc2/Eqs/pair_lj_soft.tex
deleted file mode 100644
index e32f11f0aa..0000000000
--- a/doc/doc2/Eqs/pair_lj_soft.tex
+++ /dev/null
@@ -1,15 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[
-E = \lambda^n 4 \epsilon
-\left\{
- \frac{1}{ \left[ \alpha_{\mathrm{LJ}} (1-\lambda)^2 +
- \left( \displaystyle\frac{r}{\sigma} \right)^6 \right]^2 } -
- \frac{1}{ \alpha_{\mathrm{LJ}} (1-\lambda)^2 +
- \left( \displaystyle\frac{r}{\sigma} \right)^6 }
-\right\} \qquad r < r_c
- \]
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_lubricate.jpg b/doc/doc2/Eqs/pair_lubricate.jpg
deleted file mode 100644
index 560591765a..0000000000
Binary files a/doc/doc2/Eqs/pair_lubricate.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_lubricate.tex b/doc/doc2/Eqs/pair_lubricate.tex
deleted file mode 100644
index c7e3dd96ed..0000000000
--- a/doc/doc2/Eqs/pair_lubricate.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- W & = & - a_{sq} | (v_1 - v_2) \bullet \mathbf{nn} |^2 -
- a_{sh} | (\omega_1 + \omega_2) \bullet
- (\mathbf{I} - \mathbf{nn}) - 2 \Omega_N |^2 - \\
- & & a_{pu} | (\omega_1 - \omega_2) \bullet (\mathbf{I} - \mathbf{nn}) |^2 -
- a_{tw} | (\omega_1 - \omega_2) \bullet \mathbf{nn} |^2 \qquad r < r_c
-\end{eqnarray*}
-
-$$
-\Omega_N = \mathbf{n} \times (v_1 - v_2) / r
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_meam.jpg b/doc/doc2/Eqs/pair_meam.jpg
deleted file mode 100644
index f6de50a998..0000000000
Binary files a/doc/doc2/Eqs/pair_meam.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_meam.tex b/doc/doc2/Eqs/pair_meam.tex
deleted file mode 100644
index cb9bb1702e..0000000000
--- a/doc/doc2/Eqs/pair_meam.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \sum_i \left\{ F_i(\bar{\rho}_i)
- + \frac{1}{2} \sum_{i \neq j} \phi_{ij} (r_{ij}) \right\}
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_meam_spline.jpg b/doc/doc2/Eqs/pair_meam_spline.jpg
deleted file mode 100644
index 29f1c72543..0000000000
Binary files a/doc/doc2/Eqs/pair_meam_spline.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_meam_spline.tex b/doc/doc2/Eqs/pair_meam_spline.tex
deleted file mode 100644
index 55d42f801c..0000000000
--- a/doc/doc2/Eqs/pair_meam_spline.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E=\sum_{ij}\phi(r_{ij})+\sum_{i}U(\rho_{i}),
-$$
-
-$$
- \rho_{i}=\sum_{j}\rho(r_{ij})+\sum_{jk}f(r_{ij})f(r_{ik})g[\cos(\theta_{jik})]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_meam_sw_spline.jpg b/doc/doc2/Eqs/pair_meam_sw_spline.jpg
deleted file mode 100644
index 80078999d7..0000000000
Binary files a/doc/doc2/Eqs/pair_meam_sw_spline.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_meam_sw_spline.tex b/doc/doc2/Eqs/pair_meam_sw_spline.tex
deleted file mode 100644
index 28abc433b5..0000000000
--- a/doc/doc2/Eqs/pair_meam_sw_spline.tex
+++ /dev/null
@@ -1,23 +0,0 @@
-\documentclass[showpacs,amsmath,amssymb,prb]{revtex4}
-
-
-\usepackage{graphicx}
-\usepackage{dcolumn}
-\usepackage{bm}
-
-\newcommand{\etal}{{\em et al.}}
-\newcommand{\OO}{{\mathcal{O}}}
-\newtheorem{theorem}{Theorem}
-
-\begin{document}
-
-\begin{eqnarray}
-E & = & E_{MEAM} + E_{SW} \nonumber \\
-E_{MEAM} & = & \sum _{IJ} \phi (r_{IJ}) + \sum _{I} U(\rho _I) \nonumber \\
-E_{SW} & = & \sum _{I} \sum _{JK} F(r_{IJ}) \, F(r_{IK}) \, G(\cos(\theta _{JIK})) \nonumber \\
-\rho _I & = & \sum _J \rho(r_{IJ}) + \sum _{JK} f(r_{IJ}) \, f(r_{IK}) \, g(\cos(\theta _{JIK})) \nonumber
-\end{eqnarray}
-
-\end{document}
-
-
diff --git a/doc/doc2/Eqs/pair_mgpt.jpg b/doc/doc2/Eqs/pair_mgpt.jpg
deleted file mode 100644
index 2bede7f90f..0000000000
Binary files a/doc/doc2/Eqs/pair_mgpt.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_mgpt.tex b/doc/doc2/Eqs/pair_mgpt.tex
deleted file mode 100644
index 9c314df916..0000000000
--- a/doc/doc2/Eqs/pair_mgpt.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega )
- + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega )
- + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega )
- + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega )
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_mie.jpg b/doc/doc2/Eqs/pair_mie.jpg
deleted file mode 100644
index 05a8221a93..0000000000
Binary files a/doc/doc2/Eqs/pair_mie.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_mie.tex b/doc/doc2/Eqs/pair_mie.tex
deleted file mode 100644
index 2702ce9bcf..0000000000
--- a/doc/doc2/Eqs/pair_mie.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right]
- \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_mie2.jpg b/doc/doc2/Eqs/pair_mie2.jpg
deleted file mode 100644
index 216ca1554a..0000000000
Binary files a/doc/doc2/Eqs/pair_mie2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_mie2.tex b/doc/doc2/Eqs/pair_mie2.tex
deleted file mode 100644
index 2ee9e9b34e..0000000000
--- a/doc/doc2/Eqs/pair_mie2.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- C = \left(\frac{\gamma_{rep}}{\gamma_{rep}-\gamma_{att}}\right) \left(\frac{\gamma_{rep}}{\gamma_{att}}\right)^{\left(\frac{\gamma_{att}}{\gamma_{rep}-\gamma_{att}}\right)}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_morse.jpg b/doc/doc2/Eqs/pair_morse.jpg
deleted file mode 100644
index 5ebcdb2e1d..0000000000
Binary files a/doc/doc2/Eqs/pair_morse.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_morse.tex b/doc/doc2/Eqs/pair_morse.tex
deleted file mode 100644
index 21204daa20..0000000000
--- a/doc/doc2/Eqs/pair_morse.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
- \qquad r < r_c
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_nb3b_harmonic.jpg b/doc/doc2/Eqs/pair_nb3b_harmonic.jpg
deleted file mode 100644
index c8d23da042..0000000000
Binary files a/doc/doc2/Eqs/pair_nb3b_harmonic.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_nb3b_harmonic.tex b/doc/doc2/Eqs/pair_nb3b_harmonic.tex
deleted file mode 100644
index 7f7aa8078e..0000000000
--- a/doc/doc2/Eqs/pair_nb3b_harmonic.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = K (\theta - \theta_0)^2
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_nm.jpg b/doc/doc2/Eqs/pair_nm.jpg
deleted file mode 100644
index 1e7fe0981c..0000000000
Binary files a/doc/doc2/Eqs/pair_nm.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_nm.tex b/doc/doc2/Eqs/pair_nm.tex
deleted file mode 100644
index 4adf9331cc..0000000000
--- a/doc/doc2/Eqs/pair_nm.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- E = \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n -
- n \left(\frac{r_0}{r}\right)^m \right] \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_resquared.jpg b/doc/doc2/Eqs/pair_resquared.jpg
deleted file mode 100644
index c290c68dfd..0000000000
Binary files a/doc/doc2/Eqs/pair_resquared.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_resquared.tex b/doc/doc2/Eqs/pair_resquared.tex
deleted file mode 100644
index e5c758aec0..0000000000
--- a/doc/doc2/Eqs/pair_resquared.tex
+++ /dev/null
@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ A_{12} = 4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3)^2 $$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_resquared2.jpg b/doc/doc2/Eqs/pair_resquared2.jpg
deleted file mode 100644
index d2ed21a62a..0000000000
Binary files a/doc/doc2/Eqs/pair_resquared2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_resquared2.tex b/doc/doc2/Eqs/pair_resquared2.tex
deleted file mode 100644
index ff2c3ca749..0000000000
--- a/doc/doc2/Eqs/pair_resquared2.tex
+++ /dev/null
@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ A_{12} = 4\pi^2\epsilon_{\mathrm{LJ}}(\rho\sigma^3) $$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_resquared3.jpg b/doc/doc2/Eqs/pair_resquared3.jpg
deleted file mode 100644
index 3916062a1c..0000000000
Binary files a/doc/doc2/Eqs/pair_resquared3.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_resquared3.tex b/doc/doc2/Eqs/pair_resquared3.tex
deleted file mode 100644
index 136bcf73dc..0000000000
--- a/doc/doc2/Eqs/pair_resquared3.tex
+++ /dev/null
@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ A_{12} = \epsilon_{\mathrm{LJ}} $$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_resquared4.jpg b/doc/doc2/Eqs/pair_resquared4.jpg
deleted file mode 100644
index 79ad067fa7..0000000000
Binary files a/doc/doc2/Eqs/pair_resquared4.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_resquared4.tex b/doc/doc2/Eqs/pair_resquared4.tex
deleted file mode 100644
index 6efb755774..0000000000
--- a/doc/doc2/Eqs/pair_resquared4.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ \epsilon_a = \sigma \cdot { \frac{a}{ b \cdot c } }; \epsilon_b =
-\sigma \cdot { \frac{b}{ a \cdot c } }; \epsilon_c = \sigma \cdot {
-\frac{c}{ a \cdot b } } $$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_smtbq1.jpg b/doc/doc2/Eqs/pair_smtbq1.jpg
deleted file mode 100644
index 6bfb07b778..0000000000
Binary files a/doc/doc2/Eqs/pair_smtbq1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_smtbq1.tex b/doc/doc2/Eqs/pair_smtbq1.tex
deleted file mode 100755
index 21ae0e9a49..0000000000
--- a/doc/doc2/Eqs/pair_smtbq1.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-E_{tot} & = & E_{ES} + E_{OO} + E_{MO} \\
-E_{ES} & = & \sum_i{\Big[ \chi_{i}^{0}Q_i + \frac{1}{2}J_{i}^{0}Q_{i}^{2} +
- \frac{1}{2} \sum_{j\neq i}{ J_{ij}(r_{ij})f_{cut}^{R_{coul}}(r_{ij})Q_i Q_j } \Big] } \\
-E_{OO} & = & \sum_{i,j}^{i,j = O}{\Bigg[Cexp( -\frac{r_{ij}}{\rho} ) - Df_{cut}^{r_1^{OO}r_2^{OO}}(r_{ij}) exp(Br_{ij})\Bigg]} \\
-E_{MO} & = & \sum_i{E_{cov}^{i} + \sum_{j\neq i}{ Af_{cut}^{r_{c1}r_{c2}}(r_{ij})exp\Big[-p(\frac{r_{ij}}{r_0} -1) \Big] } } \\
-\end{eqnarray*}
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_smtbq2.jpg b/doc/doc2/Eqs/pair_smtbq2.jpg
deleted file mode 100644
index 0e20248788..0000000000
Binary files a/doc/doc2/Eqs/pair_smtbq2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_smtbq2.tex b/doc/doc2/Eqs/pair_smtbq2.tex
deleted file mode 100755
index 8524c2586c..0000000000
--- a/doc/doc2/Eqs/pair_smtbq2.tex
+++ /dev/null
@@ -1,12 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-E_{cov}^{i(i=M,O)} & = & - \Bigg\{\eta_i(\mu \xi^{0})^2 f_{cut}^{r_{c1}r_{c2}}(r_{ij})
-\Bigg( \sum_{j(j=O,M)}{ exp[ -2q(\frac{r_{ij}}{r_0} - 1)] } \Bigg)
-\delta Q_i \Big( 2\frac{n_0}{\eta_i} - \delta Q_i \Big) \Bigg\}^{1/2} \\
-\delta Q_i & = & | Q_i^{F} | - | Q_i |
-\end{eqnarray*}
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_smtbq3.jpg b/doc/doc2/Eqs/pair_smtbq3.jpg
deleted file mode 100644
index 1d60459165..0000000000
Binary files a/doc/doc2/Eqs/pair_smtbq3.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_smtbq3.tex b/doc/doc2/Eqs/pair_smtbq3.tex
deleted file mode 100755
index 5bc6e465d1..0000000000
--- a/doc/doc2/Eqs/pair_smtbq3.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\xi^0 & = & \frac{\xi_O}{m} = \frac{\xi_C}{n} \\
-\frac{\beta_O}{\sqrt{m}} & = & \frac{\beta_C}{\sqrt{n}} = \xi^0 \frac{\sqrt{m}+\sqrt{n}}{2}\\
-\end{eqnarray*}
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_snap.jpg b/doc/doc2/Eqs/pair_snap.jpg
deleted file mode 100644
index af48357b5e..0000000000
Binary files a/doc/doc2/Eqs/pair_snap.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_snap.tex b/doc/doc2/Eqs/pair_snap.tex
deleted file mode 100644
index d0a17de1fb..0000000000
--- a/doc/doc2/Eqs/pair_snap.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E^i_{SNAP}(B_1^i,...,B_K^i) = \beta^{\alpha_i}_0 + \sum_{k=1}^K \beta_k^{\alpha_i} B_k^i
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_soft.jpg b/doc/doc2/Eqs/pair_soft.jpg
deleted file mode 100644
index e8a654e1ed..0000000000
Binary files a/doc/doc2/Eqs/pair_soft.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_soft.tex b/doc/doc2/Eqs/pair_soft.tex
deleted file mode 100644
index c2db15c2ee..0000000000
--- a/doc/doc2/Eqs/pair_soft.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = A \left[ 1 + \cos\left(\frac{\pi r}{r_c}\right) \right]
- \qquad r < r_c
-$$
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_sph_ideal.jpg b/doc/doc2/Eqs/pair_sph_ideal.jpg
deleted file mode 100644
index 370b75fe94..0000000000
Binary files a/doc/doc2/Eqs/pair_sph_ideal.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_sph_ideal.tex b/doc/doc2/Eqs/pair_sph_ideal.tex
deleted file mode 100644
index 91c64f00bc..0000000000
--- a/doc/doc2/Eqs/pair_sph_ideal.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- p = (\gamma - 1) \rho e
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_sph_tait.jpg b/doc/doc2/Eqs/pair_sph_tait.jpg
deleted file mode 100644
index 8bbfe80512..0000000000
Binary files a/doc/doc2/Eqs/pair_sph_tait.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_sph_tait.tex b/doc/doc2/Eqs/pair_sph_tait.tex
deleted file mode 100644
index 4e1fa9cfed..0000000000
--- a/doc/doc2/Eqs/pair_sph_tait.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- p = B [(\frac{\rho}{\rho_0})^{\gamma} - 1]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_srp1.jpg b/doc/doc2/Eqs/pair_srp1.jpg
deleted file mode 100644
index bbbdc43e05..0000000000
Binary files a/doc/doc2/Eqs/pair_srp1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_srp1.tex b/doc/doc2/Eqs/pair_srp1.tex
deleted file mode 100644
index 45aa005d86..0000000000
--- a/doc/doc2/Eqs/pair_srp1.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- F^{SRP}_{ij} & = & C(1-r/r_c)\hat{r}_{ij} \qquad r < r_c \\
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_srp2.jpg b/doc/doc2/Eqs/pair_srp2.jpg
deleted file mode 100644
index c5d20dc212..0000000000
Binary files a/doc/doc2/Eqs/pair_srp2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_sw.jpg b/doc/doc2/Eqs/pair_sw.jpg
deleted file mode 100644
index f60f07fd27..0000000000
Binary files a/doc/doc2/Eqs/pair_sw.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_sw.tex b/doc/doc2/Eqs/pair_sw.tex
deleted file mode 100644
index ebcc39d77b..0000000000
--- a/doc/doc2/Eqs/pair_sw.tex
+++ /dev/null
@@ -1,18 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E & = & \sum_i \sum_{j > i} \phi_2 (r_{ij}) +
- \sum_i \sum_{j \neq i} \sum_{k > j}
- \phi_3 (r_{ij}, r_{ik}, \theta_{ijk}) \\
- \phi_2(r_{ij}) & = & A_{ij} \epsilon_{ij} \left[ B_{ij} (\frac{\sigma_{ij}}{r_{ij}})^{p_{ij}} -
- (\frac{\sigma_{ij}}{r_{ij}})^{q_{ij}} \right]
- \exp \left( \frac{\sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right) \\
- \phi_3(r_{ij},r_{ik},\theta_{ijk}) & = & \lambda_{ijk} \epsilon_{ijk} \left[ \cos \theta_{ijk} -
- \cos \theta_{0ijk} \right]^2
- \exp \left( \frac{\gamma_{ij} \sigma_{ij}}{r_{ij} - a_{ij} \sigma_{ij}} \right)
- \exp \left( \frac{\gamma_{ik} \sigma_{ik}}{r_{ik} - a_{ik} \sigma_{ik}} \right)
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_tersoff.jpg b/doc/doc2/Eqs/pair_tersoff.jpg
deleted file mode 100644
index bd3e147192..0000000000
Binary files a/doc/doc2/Eqs/pair_tersoff.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_tersoff_1.jpg b/doc/doc2/Eqs/pair_tersoff_1.jpg
deleted file mode 100644
index 79600b499c..0000000000
Binary files a/doc/doc2/Eqs/pair_tersoff_1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_tersoff_1.tex b/doc/doc2/Eqs/pair_tersoff_1.tex
deleted file mode 100644
index 7d34712491..0000000000
--- a/doc/doc2/Eqs/pair_tersoff_1.tex
+++ /dev/null
@@ -1,24 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
- V_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
- f_C(r) & = & \left\{ \begin{array} {r@{\quad:\quad}l}
- 1 & r < R - D \\
- \frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) &
- R-D < r < R + D \\
- 0 & r > R + D
- \end{array} \right. \\
- f_R(r) & = & A \exp (-\lambda_1 r) \\
- f_A(r) & = & -B \exp (-\lambda_2 r) \\
- b_{ij} & = & \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\
- \zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
- \exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\
- g(\theta) & = & \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} -
- \frac{c^2}{\left[ d^2 +
- (\cos \theta - \cos \theta_0)^2\right]} \right)
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_tersoff_2.jpg b/doc/doc2/Eqs/pair_tersoff_2.jpg
deleted file mode 100644
index 6cb8778a09..0000000000
Binary files a/doc/doc2/Eqs/pair_tersoff_2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_tersoff_2.tex b/doc/doc2/Eqs/pair_tersoff_2.tex
deleted file mode 100644
index 7b5beb8ef3..0000000000
--- a/doc/doc2/Eqs/pair_tersoff_2.tex
+++ /dev/null
@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\lambda_1^{i,j} &=& \frac{1}{2}(\lambda_1^i + \lambda_1^j)\\
-\lambda_2^{i,j} &=& \frac{1}{2}(\lambda_2^i + \lambda_2^j)\\
-A_{i,j} &=& (A_{i}A_{j})^{1/2}\\
-B_{i,j} &=& \chi_{ij}(B_{i}B_{j})^{1/2}\\
-R_{i,j} &=& (R_{i}R_{j})^{1/2}\\
-S_{i,j} &=& (S_{i}S_{j})^{1/2}\\
-\end{eqnarray*}
-
-\end{document}
\ No newline at end of file
diff --git a/doc/doc2/Eqs/pair_tersoff_mod.jpg b/doc/doc2/Eqs/pair_tersoff_mod.jpg
deleted file mode 100644
index 2618943d85..0000000000
Binary files a/doc/doc2/Eqs/pair_tersoff_mod.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_tersoff_mod.tex b/doc/doc2/Eqs/pair_tersoff_mod.tex
deleted file mode 100644
index eafc4fdeeb..0000000000
--- a/doc/doc2/Eqs/pair_tersoff_mod.tex
+++ /dev/null
@@ -1,24 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
- V_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
- f_C(r) & = & \left\{ \begin{array} {r@{\quad:\quad}l}
- 1 & r < R - D \\
- \frac{1}{2} - \frac{9}{16} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) - \frac{1}{16} \sin \left( \frac{3\pi}{2} \frac{r-R}{D} \right) &
- R-D < r < R + D \\
- 0 & r > R + D
- \end{array} \right. \\
- f_R(r) & = & A \exp (-\lambda_1 r) \\
- f_A(r) & = & -B \exp (-\lambda_2 r) \\
- b_{ij} & = & \left( 1 + {\zeta_{ij}}^\eta \right)^{-\frac{1}{2n}} \\
- \zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
- \exp \left[ \alpha (r_{ij} - r_{ik})^\beta \right] \\
- g(\theta) & = & c_1 + g_o(\theta) g_a(\theta) \\
- g_o(\theta) & = & \frac{c_2 (h - \cos \theta)^2}{c_3 + (h - \cos \theta)^2} \\
- g_a(\theta) & = & 1 + c_4 \exp \left[ -c_5 (h - \cos \theta)^2 \right] \\
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_tersoff_zbl.jpg b/doc/doc2/Eqs/pair_tersoff_zbl.jpg
deleted file mode 100644
index 20d60d2256..0000000000
Binary files a/doc/doc2/Eqs/pair_tersoff_zbl.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_tersoff_zbl.tex b/doc/doc2/Eqs/pair_tersoff_zbl.tex
deleted file mode 100644
index 902819aa1b..0000000000
--- a/doc/doc2/Eqs/pair_tersoff_zbl.tex
+++ /dev/null
@@ -1,33 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
- V_{ij} & = & (1 - f_F(r_{ij})) V^{ZBL}_{ij} + f_F(r_{ij}) V^{Tersoff}_{ij} \\
-f_F(r_{ij}) & = & \frac{1}{1 + e^{-A_F(r_{ij} - r_C)}}\\
- \\
- \\
- V^{ZBL}_{ij} & = & \frac{1}{4\pi\epsilon_0} \frac{Z_1 Z_2 \,e^2}{r_{ij}} \phi(r_{ij}/a) \\
- a & = & \frac{0.8854\,a_0}{Z_{1}^{0.23} + Z_{2}^{0.23}}\\
- \phi(x) & = & 0.1818e^{-3.2x} + 0.5099e^{-0.9423x} + 0.2802e^{-0.4029x} + 0.02817e^{-0.2016x}\\
- \\
- \\
- V^{Tersoff}_{ij} & = & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) \right] \\
- f_C(r) & = & \left\{ \begin{array} {r@{\quad:\quad}l}
- 1 & r < R - D \\
- \frac{1}{2} - \frac{1}{2} \sin \left( \frac{\pi}{2} \frac{r-R}{D} \right) &
- R-D < r < R + D \\
- 0 & r > R + D
- \end{array} \right. \\
- f_R(r) & = & A \exp (-\lambda_1 r) \\
- f_A(r) & = & -B \exp (-\lambda_2 r) \\
- b_{ij} & = & \left( 1 + \beta^n {\zeta_{ij}}^n \right)^{-\frac{1}{2n}} \\
- \zeta_{ij} & = & \sum_{k \neq i,j} f_C(r_{ik}) g(\theta_{ijk})
- \exp \left[ {\lambda_3}^m (r_{ij} - r_{ik})^m \right] \\
- g(\theta) & = & \gamma_{ijk} \left( 1 + \frac{c^2}{d^2} -
- \frac{c^2}{\left[ d^2 +
- (\cos \theta - \cos \theta_0)^2\right]} \right)
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_vashishta.jpg b/doc/doc2/Eqs/pair_vashishta.jpg
deleted file mode 100644
index ca5f118a87..0000000000
Binary files a/doc/doc2/Eqs/pair_vashishta.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_vashishta.tex b/doc/doc2/Eqs/pair_vashishta.tex
deleted file mode 100644
index b65056a254..0000000000
--- a/doc/doc2/Eqs/pair_vashishta.tex
+++ /dev/null
@@ -1,22 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- U & = & \sum_i^N \sum_{j > i}^N U_{ij}^{(2)} (r_{ij}) +
- \sum_i^N \sum_{j \neq i}^N \sum_{k > j, k \neq i}^N
- U_{ijk}^{(3)} (r_{ij}, r_{ik}, \theta_{ijk})
- \\
- U_{ij}^{(2)} (r) & = & \frac{H_{ij}}{r^{\eta_{ij}}}
- + \frac{Z_i Z_j}{r}\exp(-r/\lambda_{1,ij})
- - \frac{D_{ij}}{r^4}\exp(-r/\lambda_{4,ij})
- - \frac{W_{ij}}{r^6}, r < r_{c,{ij}}
- \\
- U_{ijk}^{(3)}(r_{ij},r_{ik},\theta_{ijk}) & = & B_{ijk}
- \frac{\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2}
- {1+C_{ijk}\left[ \cos \theta_{ijk} - \cos \theta_{0ijk} \right]^2} \times \\
-& & \exp \left( \frac{\gamma_{ij}}{r_{ij} - r_{0,ij}} \right)
- \exp \left( \frac{\gamma_{ik}}{r_{ik} - r_{0,ik}} \right), r_{ij} < r_{0,ij}, r_{ik} < r_{0,ik}
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_yukawa.jpg b/doc/doc2/Eqs/pair_yukawa.jpg
deleted file mode 100644
index 103edc6043..0000000000
Binary files a/doc/doc2/Eqs/pair_yukawa.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_yukawa.tex b/doc/doc2/Eqs/pair_yukawa.tex
deleted file mode 100644
index 382cf249a8..0000000000
--- a/doc/doc2/Eqs/pair_yukawa.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = A \frac{e^{- \kappa r}}{r} \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_yukawa_colloid.jpg b/doc/doc2/Eqs/pair_yukawa_colloid.jpg
deleted file mode 100644
index 1d83624757..0000000000
Binary files a/doc/doc2/Eqs/pair_yukawa_colloid.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_yukawa_colloid.tex b/doc/doc2/Eqs/pair_yukawa_colloid.tex
deleted file mode 100644
index dbdbbcd140..0000000000
--- a/doc/doc2/Eqs/pair_yukawa_colloid.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
- E = \frac{A}{\kappa} e^{- \kappa (r - (r_i + r_j))} \qquad r < r_c
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/pair_zbl.jpg b/doc/doc2/Eqs/pair_zbl.jpg
deleted file mode 100644
index 88656af5eb..0000000000
Binary files a/doc/doc2/Eqs/pair_zbl.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/pair_zbl.tex b/doc/doc2/Eqs/pair_zbl.tex
deleted file mode 100644
index 3d68dbed23..0000000000
--- a/doc/doc2/Eqs/pair_zbl.tex
+++ /dev/null
@@ -1,11 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
- E^{ZBL}_{ij} & = & \frac{1}{4\pi\epsilon_0} \frac{Z_i Z_j \,e^2}{r_{ij}} \phi(r_{ij}/a)+ S(r_{ij})\\
- a & = & \frac{0.46850}{Z_{i}^{0.23} + Z_{j}^{0.23}}\\
- \phi(x) & = & 0.18175e^{-3.19980x} + 0.50986e^{-0.94229x} + 0.28022e^{-0.40290x} + 0.02817e^{-0.20162x}\\
- \end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/polymorphic1.jpg b/doc/doc2/Eqs/polymorphic1.jpg
deleted file mode 100644
index 4757cb7ad8..0000000000
Binary files a/doc/doc2/Eqs/polymorphic1.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/polymorphic1.tex b/doc/doc2/Eqs/polymorphic1.tex
deleted file mode 100644
index b4b925ccf8..0000000000
--- a/doc/doc2/Eqs/polymorphic1.tex
+++ /dev/null
@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-E=\frac{1}{2}\sum_{i=1}^{i=N}\sum_{j=1}^{j=N}\left[\left(1-\delta_{ij}\right)\cdot U_{IJ}\left(r_{ij}\right)-\left(1-\eta_{ij}\right)\cdot F_{IJ}\left(r_{ij}\right)\cdot V_{IJ}\left(r_{ij}\right)\right]
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/polymorphic2.jpg b/doc/doc2/Eqs/polymorphic2.jpg
deleted file mode 100644
index 05133f4849..0000000000
Binary files a/doc/doc2/Eqs/polymorphic2.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/polymorphic2.tex b/doc/doc2/Eqs/polymorphic2.tex
deleted file mode 100644
index 80b1c93821..0000000000
--- a/doc/doc2/Eqs/polymorphic2.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-X_{ij}=\sum_{k=i_1,k\neq i,j}^{i_N}W_{IK}\left(r_{ik}\right)\cdot G_{JIK}\left(\theta_{jik}\right)\cdot P_{IK}\left(\Delta r_{jik}\right)
-\label{X_eq2}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/polymorphic3.jpg b/doc/doc2/Eqs/polymorphic3.jpg
deleted file mode 100644
index ba748e63c5..0000000000
Binary files a/doc/doc2/Eqs/polymorphic3.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/polymorphic3.tex b/doc/doc2/Eqs/polymorphic3.tex
deleted file mode 100644
index 71db8d81b0..0000000000
--- a/doc/doc2/Eqs/polymorphic3.tex
+++ /dev/null
@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-\Delta r_{jik}=r_{ij}-\xi_{IJ}\cdot r_{ik}
-\label{Dr_eq3}
-$$
-
-\end{document}
diff --git a/doc/doc2/Eqs/polymorphic4.jpg b/doc/doc2/Eqs/polymorphic4.jpg
deleted file mode 100644
index 7a094d6a21..0000000000
Binary files a/doc/doc2/Eqs/polymorphic4.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/polymorphic4.tex b/doc/doc2/Eqs/polymorphic4.tex
deleted file mode 100644
index b792df82a0..0000000000
--- a/doc/doc2/Eqs/polymorphic4.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\left\{\begin{array}{l}
-\eta_{ij}=\delta_{ij},\xi_{IJ}=0 \\
-U_{IJ}\left(r\right)=A_{IJ}\cdot\epsilon_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^q\cdot \left[B_{IJ}\cdot \left(\frac{\sigma_{IJ}}{r}\right)^{p-q}-1\right]\cdot exp\left(\frac{\sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
-V_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
-F_{IJ}\left(X\right)=-X \\
-P_{IJ}\left(\Delta r\right)=1 \\
-W_{IJ}\left(r\right)=\sqrt{\lambda_{IJ}\cdot \epsilon_{IJ}}\cdot exp\left(\frac{\gamma_{IJ}\cdot \sigma_{IJ}}{r-a_{IJ}\cdot \sigma_{IJ}}\right) \\
-G_{JIK}\left(\theta\right)=\left(cos\theta+\frac{1}{3}\right)^2
-\end{array}\right.
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/polymorphic5.jpg b/doc/doc2/Eqs/polymorphic5.jpg
deleted file mode 100644
index 500238b2a9..0000000000
Binary files a/doc/doc2/Eqs/polymorphic5.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/polymorphic5.tex b/doc/doc2/Eqs/polymorphic5.tex
deleted file mode 100644
index a5451b98d6..0000000000
--- a/doc/doc2/Eqs/polymorphic5.tex
+++ /dev/null
@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-\left\{\begin{array}{l}
-\eta_{ij}=\delta_{ij},\xi_{IJ}=1 \\
-U_{IJ}\left(r\right)=\frac{D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{2S_{IJ}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\
-V_{IJ}\left(r\right)=\frac{S_{IJ}\cdot D_{e,IJ}}{S_{IJ}-1}\cdot exp\left[-\beta_{IJ}\sqrt{\frac{2}{S_{IJ}}\left(r-r_{e,IJ}\right)}\right]\cdot f_{c,IJ}\left(r\right) \\
-F_{IJ}\left(X\right)=\left(1+X\right)^{-\frac{1}{2}} \\
-P_{IJ}\left(\Delta r\right)=exp\left(2\mu_{IK}\cdot \Delta r\right) \\
-W_{IJ}\left(r\right)=f_{c,IK}\left(r\right) \\
-G_{JIK}\left(\theta\right)=\gamma_{IK}\left[1+\frac{c_{IK}^2}{d_{IK}^2}-\frac{c_{IK}^2}{d_{IK}^2+\left(h_{IK}+cos\theta\right)^2}\right]
-\end{array}\right.
-\end{eqnarray*}
-
-\end{document}
diff --git a/doc/doc2/Eqs/polymorphic6.jpg b/doc/doc2/Eqs/polymorphic6.jpg
deleted file mode 100644
index 65ea78bf21..0000000000
Binary files a/doc/doc2/Eqs/polymorphic6.jpg and /dev/null differ
diff --git a/doc/doc2/Eqs/polymorphic6.tex b/doc/doc2/Eqs/polymorphic6.tex
deleted file mode 100644
index c8f9f2f25b..0000000000
--- a/doc/doc2/Eqs/polymorphic6.tex
+++ /dev/null
@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-f_{c,IJ}=\left\{\begin{array}{lr}
-1, & r\leq r_{s,IJ} \\
-\frac{1}{2}+\frac{1}{2} cos \left[\frac{\pi \left(r-r_{s,IJ}\right)}{r_{c,IJ}-r_{s,IJ}}\right], & r_{s,IJ}
-
-
-LAMMPS Users Manual
-
-
-
-
-
-
-
-
-
-LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands
-
-
-
-
-
-
-
-
-
-
-
-LAMMPS Documentation
-
-10 Aug 2015 version
-
-Version info:
-
-The LAMMPS "version" is the date when it was released, such as 1 May
-2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
-feature, we release it immediately, and post a notice on this page of
-the WWW site. Each dated copy of LAMMPS contains all the
-features and bug-fixes up to and including that version date. The
-version date is printed to the screen and logfile every time you run
-LAMMPS. It is also in the file src/version.h and in the LAMMPS
-directory name created when you unpack a tarball, and at the top of
-the first page of the manual (this page).
-
-- If you browse the HTML doc pages on the LAMMPS WWW site, they always
-describe the most current version of LAMMPS.
-
-
- If you browse the HTML doc pages included in your tarball, they
-describe the version you have.
-
-
- The PDF file on the WWW site or in the tarball is updated
-about once per month. This is because it is large, and we don't want
-it to be part of every patch.
-
-
- There is also a Developer.pdf file in the doc
-directory, which describes the internal structure and algorithms of
-LAMMPS.
-
-LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
-Simulator.
-
-LAMMPS is a classical molecular dynamics simulation code designed to
-run efficiently on parallel computers. It was developed at Sandia
-National Laboratories, a US Department of Energy facility, with
-funding from the DOE. It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL).
-
-The primary developers of LAMMPS are Steve Plimpton, Aidan
-Thompson, and Paul Crozier who can be contacted at
-sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at
-http://lammps.sandia.gov has more information about the code and its
-uses.
-
-
-
-
-
-
-
-The LAMMPS documentation is organized into the following sections. If
-you find errors or omissions in this manual or have suggestions for
-useful information to add, please send an email to the developers so
-we can improve the LAMMPS documentation.
-
-Once you are familiar with LAMMPS, you may want to bookmark this
-page at Section_commands.html#comm since
-it gives quick access to documentation for all LAMMPS commands.
-
-PDF file of the entire manual, generated by
-htmldoc
-
-
-
--
-Introduction
-
-
-
- Getting started
-
-
-
- Commands
-
-
-
- Packages
-
-
-
- Accelerating LAMMPS performance
-
-
-
- How-to discussions
-
-
-
- Example problems
-
-
- Performance & scalability
-
-
- Additional tools
-
-
- Modifying & extending LAMMPS
-
-
-
- Python interface
-
-
-
- Errors
-
-
-
- Future and history
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-