Merge branch 'master' into add-user-reaxc-omp

pdf: utils/txt2html/txt2html.exe

	@(\

		set -e; \

		cd src; \

		../utils/txt2html/txt2html.exe -b *.txt; \

		htmldoc --batch lammps.book;          \

If the {quadratic} keyword value is set to 1, then additional

columns are appended to each per-atom array, corresponding to

a matrix of quantities that are products of two bispectrum components. If the

number of bispectrum components is {K}, then the number of matrix elements

is {K}^2. These are output in subblocks of {K}^2 columns, using the same

ordering of columns and sub-blocks as was used for the bispectrum

components.

the products of all distinct pairs of  bispectrum components. If the

number of bispectrum components is {K}, then the number of distinct pairs

is  {K}({K}+1)/2. These are output in subblocks of  {K}({K}+1)/2 columns, using the same

ordering of sub-blocks as was used for the bispectrum

components. Within each sub-block, the ordering is upper-triangular,

(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K})

These values can be accessed by any command that uses per-atom values

from a compute as input.  See "Section

dihedral_coeff 1 3  69.3   1 93.9 1    1 90   0    1 90   0  &

                    49.1   0 0.00 0    1 74.4 1    0 0.00 0  &

                    25.2   0 0.00 0    0 0.00 0    1 48.1 1

:pre

[Description:]

\(F_r'\) is a random force proportional to

\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\}

                 \{\mathrm dt\, \mathtt\{damp\_com\} \}

        \} \). :b

        \} \).

\(f_r'\) is a random force proportional to

\(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\}

                 \{\mathrm dt\, \mathtt\{damp\_drude\} \}

        \} \). :b

        \} \).

Then the real forces acting on the particles are computed from the inverse

transform:

\begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\}

plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x.

sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R

supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R

spine @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ An approximation to a dendtritic spine

spine_two @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ Another approximation to a dendtritic spine

spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ An approximation to a dendtritic spine

spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise  @ Another approximation to a dendtritic spine

thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB

torus @ R r  @  (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2  @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@)