A prism region used with the create_box command must have tilt -factors (xy,xz,yz) that do not skew the box more than half the -distance of the parallel box length. For example, if xlo = 2 and xhi -= 12, then the x box length is 10 and the xy tilt factor must be +
By default, a prism region used with the create_box command must +have tilt factors (xy,xz,yz) that do not skew the box more than half +the distance of the parallel box length. For example, if xlo = 2 and +xhi = 12, then the x box length is 10 and the xy tilt factor must be between -5 and 5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all -geometrically equivalent. +geometrically equivalent. If you wish to define a box with tilt +factors that exceed these limits, you can use the box tilt +command, with a setting of large; a setting of small is the +default.
See Section_howto 12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations.
-When a prism region is used, the simulation domain must be periodic in -any dimensions with a non-zero tilt factor, as defined by the -boundary command. I.e. if the xy tilt factor is -non-zero, then both the x and y dimensions must be periodic. -Similarly, x and z must be periodic if xz is non-zero and y and z must -be periodic if yz is non-zero. Also note that if your simulation will -tilt the box, e.g. via the fix deform command, the -simulation box must be defined as triclinic, even if the tilt factors -are initially 0.0. +
When a prism region is used, the simulation domain should normally be +periodic in the dimension that the tilt is applied to, which is given +by the second dimension of the tilt factor (e.g. y for xy tilt). This +is so that pairs of atoms interacting across that boundary will have +one of them shifted by the tilt factor. Periodicity is set by the +boundary command. For example, if the xy tilt factor +is non-zero, then the y dimension should be periodic. Similarly, the +z dimension should be periodic if xz or yz is non-zero. LAMMPS does +not require this periodicity, but you may lose atoms if this is not +the case. +
+Also note that if your simulation will tilt the box, e.g. via the fix +deform command, the simulation box must be setup to +be triclinic, even if the tilt factors are initially 0.0. You can +also change an orthogonal box to a triclinic box or vice versa by +using the change box command with its ortho and +triclinic options.
IMPORTANT NOTE: If the system is non-periodic (in a dimension), then you should not make the lo/hi box dimensions (as defined in your diff --git a/doc/create_box.txt b/doc/create_box.txt index 8d4dbdf906..94e65dae80 100644 --- a/doc/create_box.txt +++ b/doc/create_box.txt @@ -60,30 +60,41 @@ positive or negative values and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelipiped. -A {prism} region used with the create_box command must have tilt -factors (xy,xz,yz) that do not skew the box more than half the -distance of the parallel box length. For example, if xlo = 2 and xhi -= 12, then the x box length is 10 and the xy tilt factor must be +By default, a {prism} region used with the create_box command must +have tilt factors (xy,xz,yz) that do not skew the box more than half +the distance of the parallel box length. For example, if xlo = 2 and +xhi = 12, then the x box length is 10 and the xy tilt factor must be between -5 and 5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation, since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all -geometrically equivalent. +geometrically equivalent. If you wish to define a box with tilt +factors that exceed these limits, you can use the "box tilt"_box.html +command, with a setting of {large}; a setting of {small} is the +default. See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. -When a prism region is used, the simulation domain must be periodic in -any dimensions with a non-zero tilt factor, as defined by the -"boundary"_boundary.html command. I.e. if the xy tilt factor is -non-zero, then both the x and y dimensions must be periodic. -Similarly, x and z must be periodic if xz is non-zero and y and z must -be periodic if yz is non-zero. Also note that if your simulation will -tilt the box, e.g. via the "fix deform"_fix_deform.html command, the -simulation box must be defined as triclinic, even if the tilt factors -are initially 0.0. +When a prism region is used, the simulation domain should normally be +periodic in the dimension that the tilt is applied to, which is given +by the second dimension of the tilt factor (e.g. y for xy tilt). This +is so that pairs of atoms interacting across that boundary will have +one of them shifted by the tilt factor. Periodicity is set by the +"boundary"_boundary.html command. For example, if the xy tilt factor +is non-zero, then the y dimension should be periodic. Similarly, the +z dimension should be periodic if xz or yz is non-zero. LAMMPS does +not require this periodicity, but you may lose atoms if this is not +the case. + +Also note that if your simulation will tilt the box, e.g. via the "fix +deform"_fix_deform.html command, the simulation box must be setup to +be triclinic, even if the tilt factors are initially 0.0. You can +also change an orthogonal box to a triclinic box or vice versa by +using the "change box"_change_box.html command with its {ortho} and +{triclinic} options. IMPORTANT NOTE: If the system is non-periodic (in a dimension), then you should not make the lo/hi box dimensions (as defined in your diff --git a/doc/read_data.html b/doc/read_data.html index 7e76424991..c09046448f 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -141,29 +141,40 @@ and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped.
-The tilt factors (xy,xz,yz) can not skew the box more than half the -distance of the corresponding parallel box length. For example, if -xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt -factor must be between -5 and 5. Similarly, both xz and yz must be -between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a -limitation, since if the maximum tilt factor is 5 (as in this +
By default, the tilt factors (xy,xz,yz) can not skew the box more than +half the distance of the corresponding parallel box length. For +example, if xlo = 2 and xhi = 12, then the x box length is 10 and the +xy tilt factor must be between -5 and 5. Similarly, both xz and yz +must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not +a limitation, since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are all geometrically equivalent. +... are all geometrically equivalent. If you wish to define a box +with tilt factors that exceed these limits, you can use the box +tilt command, with a setting of large; a setting of +small is the default.
See Section_howto 12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations.
-When a triclinic system is used, the simulation domain must be -periodic in any dimensions with a non-zero tilt factor, as defined by -the boundary command. I.e. if the xy tilt factor is -non-zero, then both the x and y dimensions must be periodic. -Similarly, x and z must be periodic if xz is non-zero and y and z must -be periodic if yz is non-zero. Also note that if your simulation will -tilt the box, e.g. via the fix deform command, the -simulation box must be defined as triclinic, even if the tilt factors -are initially 0.0. +
When a triclinic system is used, the simulation domain should normally +be periodic in the dimension that the tilt is applied to, which is +given by the second dimension of the tilt factor (e.g. y for xy tilt). +This is so that pairs of atoms interacting across that boundary will +have one of them shifted by the tilt factor. Periodicity is set by +the boundary command. For example, if the xy tilt +factor is non-zero, then the y dimension should be periodic. +Similarly, the z dimension should be periodic if xz or yz is non-zero. +LAMMPS does not require this periodicity, but you may lose atoms if +this is not the case. +
+Also note that if your simulation will tilt the box, e.g. via the fix +deform command, the simulation box must be setup to +be triclinic, even if the tilt factors are initially 0.0. You can +also change an orthogonal box to a triclinic box or vice versa by +using the change box command with its ortho and +triclinic options.
For 2d simulations, the zlo zhi values should be set to bound the z coords for atoms that appear in the file; the default of -0.5 0.5 is diff --git a/doc/read_data.txt b/doc/read_data.txt index c5251cb5d1..4877ad61c3 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -135,29 +135,40 @@ and are called "tilt factors" because they are the amount of displacement applied to faces of an originally orthogonal box to transform it into the parallelepiped. -The tilt factors (xy,xz,yz) can not skew the box more than half the -distance of the corresponding parallel box length. For example, if -xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt -factor must be between -5 and 5. Similarly, both xz and yz must be -between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a -limitation, since if the maximum tilt factor is 5 (as in this +By default, the tilt factors (xy,xz,yz) can not skew the box more than +half the distance of the corresponding parallel box length. For +example, if xlo = 2 and xhi = 12, then the x box length is 10 and the +xy tilt factor must be between -5 and 5. Similarly, both xz and yz +must be between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not +a limitation, since if the maximum tilt factor is 5 (as in this example), then configurations with tilt = ..., -15, -5, 5, 15, 25, -... are all geometrically equivalent. +... are all geometrically equivalent. If you wish to define a box +with tilt factors that exceed these limits, you can use the "box +tilt"_box.html command, with a setting of {large}; a setting of +{small} is the default. See "Section_howto 12"_Section_howto.html#howto_12 of the doc pages for a geometric description of triclinic boxes, as defined by LAMMPS, and how to transform these parameters to and from other commonly used triclinic representations. -When a triclinic system is used, the simulation domain must be -periodic in any dimensions with a non-zero tilt factor, as defined by -the "boundary"_boundary.html command. I.e. if the xy tilt factor is -non-zero, then both the x and y dimensions must be periodic. -Similarly, x and z must be periodic if xz is non-zero and y and z must -be periodic if yz is non-zero. Also note that if your simulation will -tilt the box, e.g. via the "fix deform"_fix_deform.html command, the -simulation box must be defined as triclinic, even if the tilt factors -are initially 0.0. +When a triclinic system is used, the simulation domain should normally +be periodic in the dimension that the tilt is applied to, which is +given by the second dimension of the tilt factor (e.g. y for xy tilt). +This is so that pairs of atoms interacting across that boundary will +have one of them shifted by the tilt factor. Periodicity is set by +the "boundary"_boundary.html command. For example, if the xy tilt +factor is non-zero, then the y dimension should be periodic. +Similarly, the z dimension should be periodic if xz or yz is non-zero. +LAMMPS does not require this periodicity, but you may lose atoms if +this is not the case. + +Also note that if your simulation will tilt the box, e.g. via the "fix +deform"_fix_deform.html command, the simulation box must be setup to +be triclinic, even if the tilt factors are initially 0.0. You can +also change an orthogonal box to a triclinic box or vice versa by +using the "change box"_change_box.html command with its {ortho} and +{triclinic} options. For 2d simulations, the {zlo zhi} values should be set to bound the z coords for atoms that appear in the file; the default of -0.5 0.5 is