forked from lijiext/lammps
46 lines
8.3 KiB
Plaintext
46 lines
8.3 KiB
Plaintext
Description
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"""""""""""
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Below is a list of currently supported manifolds, their parameters and a short description of them.
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The parameters listed here are in the same order as they should be passed to the relevant fixes.
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| *manifold* | *parameters* | *equation* | *description* | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| cylinder | R | x^2 + y^2 - R^2 = 0 | Cylinder along z-axis, axis going through (0,0,0) | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| cylinder_dent | R l a | x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise | A cylinder with a dent around z = 0 | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| dumbbell | a A B c | -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 | A dumbbell | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| ellipsoid | a b c | (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 | An ellipsoid | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| plane | a b c x0 y0 z0 | a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 | A plane with normal (a,b,c) going through point (x0,y0,z0) | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| plane_wiggle | a w | z - a*sin(w*x) = 0 | A plane with a sinusoidal modulation on z along x. | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| sphere | R | x^2 + y^2 + z^2 - R^2 = 0 | A sphere of radius R | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| supersphere | R q | |x|^q + |y|^q + |z|^q - R^q = 0 | A supersphere of hyperradius R | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| 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 | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| 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 | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| thylakoid | wB LB lB | Various, see :ref:`(Paquay) <Paquay>` | A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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| 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) | |
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+---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+
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.. _Paquay:
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**(Paquay)** Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
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preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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