ParM
parm
A molecular dynamics library
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Lees-Edwards boundary conditions, with shear in the x-direction, relative to y. More...
#include <box.hpp>
Public Member Functions | |
LeesEdwardsBox (Vec size, flt gamma=0.0) | |
LeesEdwardsBox (flt L, flt gamma=0.0) | |
Vec | diff (Vec r1, Vec r2) |
Distance between two points, given boundary conditions. More... | |
virtual Vec | diff (Vec r1, Vec r2, boost::array< int, NDIM > boxes) |
virtual boost::array< int, NDIM > | box_round (Vec r1, Vec r2) |
The div function to go with diff . More... | |
flt | get_gamma () |
The current shear amount. More... | |
void | shear (flt dgamma) |
Change the shear by dgamma. More... | |
void | shear (flt dgamma, AtomGroup &atoms) |
Change the shear by dgamma, and move the atoms as necessary. More... | |
void | shear_to (flt gamma) |
Change the shear to gamma. More... | |
void | shear_to (flt gamma, AtomGroup &atoms) |
Change the shear to gamma, and move the atoms as necessary. More... | |
Vec | non_affine (Vec v) |
Vec | affine (Vec v) |
Public Member Functions inherited from OriginBox | |
OriginBox (Vec size) | |
OriginBox (flt L) | |
flt | V () |
Volume. Can return NaN. More... | |
flt | L () |
OriginBox (flt L) | |
flt | V () |
Volume. Can return NaN. More... | |
flt | L () |
flt | resize (flt factor) |
Resize by a factor. Does not move atoms. More... | |
flt | resize (flt factor, AtomGroup &atoms) |
Resize by a factor, and move atoms in the affine direction. More... | |
flt | resize_to (Vec newsize) |
Resize to a specific shape. Does not move atoms. More... | |
flt | resize_to (Vec newsize, AtomGroup &atoms) |
Resize to a specific shape, and move atoms in the affine direction. More... | |
flt | resize_to_V (flt newV) |
Resize to a specific volume. Does not move atoms. More... | |
flt | resize_to_V (flt newV, AtomGroup &atoms) |
Resize to a specific volume, and move atoms in the affine direction. More... | |
flt | resize_to_L (flt newL) |
Resize to a specific length. Does not move atoms. More... | |
flt | resize_to_L (flt newL, AtomGroup &atoms) |
Resize to a specific length, and move atoms in the affine direction. More... | |
Vec | rand_loc () |
Get a random point in the box. More... | |
Vec | box_shape () |
void | pure_shear_to (flt epsilon) |
Apply a pure shear of epsilon to reshape box. More... | |
void | pure_shear_to (flt epsilon, AtomGroup &atoms) |
Apply a pure shear of epsilon, moving atoms. More... | |
Public Member Functions inherited from Box | |
virtual | ~Box () |
Protected Attributes | |
flt | gamma |
Protected Attributes inherited from OriginBox | |
Vec | boxsize |
Lees-Edwards boundary conditions, with shear in the x-direction, relative to y.
The div
function to go with diff
.
Reimplemented from OriginBox.
Reimplemented from OriginBox.
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inline |
The current shear amount.
void LeesEdwardsBox::shear | ( | flt | dgamma | ) |
Change the shear by dgamma.
Change the shear by dgamma, and move the atoms as necessary.
void LeesEdwardsBox::shear_to | ( | flt | gamma | ) |
Change the shear to gamma.
Change the shear to gamma, and move the atoms as necessary.
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protected |