more work on read_data and doc pages
This commit is contained in:
Steve Plimpton
@ -1,29 +1,32 @@
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2d simulations
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==============
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================
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2d simulations
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================
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You must use the :doc:`dimension <dimension>` command to specify a 2d
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simulation. The default is 3d.
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Make the simulation box periodic in z via the :doc:`boundary <boundary>`
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command. This is the default.
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A 2d simulation box must be periodic in z as set by the :doc:`boundary
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<boundary>` command. This is the default.
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If using the :doc:`create_box <create_box>` command, you must define a
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simulation box which straddes z = 0.0 in the z dimension since all the
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atoms will have a z coordinate of zero. Typicaily the width of box in
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the z dimension should be narrow, e.g. -0.5 to 0.5, but that is not
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required. An example is:
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simulation box which straddles z = 0.0 in the z dimension since all
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the atoms will have a z coordinate of zero. Typicaily the width of
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box in the z dimension should be narrow, e.g. -0.5 to 0.5, but that is
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not required. Example are:
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.. code-block:: LAMMPS
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create_box 1 -10 10 0 10 -0.5 0.5
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create_box 1 -10 10 0 10 -0.25 0.25
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Likewise, If using the :doc:`read_data <read_data>` command to define
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the simulation box and read in a file of atom coordinates, the default
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"zlo zhi" values are -0.5 0.5 for 2d simulations. If the data file
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includes that header keyword the zlo/zhi values must straddle z = 0.0.
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The z coords for atoms listed in the file must be 0.0 (within epsilon
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of zero is also allowed in case the data file was generated by another
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program with finite precision).
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Likewise, if using the :doc:`read_data <read_data>` command to define
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the simulation box and read in a data file of atom coordinates, the
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default "zlo zhi" values are -0.5 0.5 for 2d simulations. If the data
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file includes that header keyword the zlo/zhi values must straddle z =
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0.0. Also, the z coord for each atom listed in the file must be 0.0.
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A value within epsilon of zero is also allowed in case the data file
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was generated by another program with finite precision, in which case
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the z coord for the atom will be set to 0.0.
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Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last fix
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defined in the input script. It ensures that the z-components of
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@ -48,13 +48,17 @@ box/relax <fix_box_relax>` command.
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A third use is to shear a bulk solid to study the response of the
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material. The :doc:`fix deform <fix_deform>` command can be used for
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this purpose. It allows dynamic control of the xy, xz, yz tilt
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factors as a simulation runs. This is discussed in the next section
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on non-equilibrium MD (NEMD) simulations.
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factors as a simulation runs. This is discussed in the :doc:`Howto
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NEMD <Howto_nemd>` doc page on non-equilibrium MD (NEMD) simulations.
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Conceptually, a triclinic parallelepiped is defined with an "origin"
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at (xlo,ylo,zhi) and 3 edge vectors **A** = (ax,ay,az), **B** =
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(bx,by,bz), **C** = (cx,cy,cz) which can now be arbitrary vectors, so
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long as they are non-zero, distinct, and not co-planar.
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(bx,by,bz), **C** = (cx,cy,cz) which can be arbitrary vectors, so long
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as they are non-zero, distinct, and not co-planar. In addition, they
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must define a right-handed system, such that (**A** cross **B**)
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points in the direction of **C**. Note that a left-handed system can
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be converted to a right-handed system by simply swapping the order of
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any two of the **A**, **B**, **C** vectors.
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The 4 commands listed above for defining orthogonal simulation boxes
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have triclinic options which allow for specification of the origin and
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@ -64,46 +68,45 @@ a *restricted* triclinic box.
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A *general* triclinic box is specified by an origin (xlo, ylo, zlo)
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and arbitrary edge vectors **A** = (ax,ay,az), **B** = (bx,by,bz), and
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**C** = (cx,cy,cz). So there are 12 parameters in total. Note that a
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general triclinic box can either be *right-handed* if (**A** x **B**)
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points in the direction of **C**, or it can be *left-handed* if (**A**
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x **B**) points opposite to **C**.
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**C** = (cx,cy,cz). So there are 12 parameters in total.
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A *restricted* triclinic box also has an origin (xlo,ylo,zlo), but its
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edge vectors are of the following form: **A** = (xhi-xlo,0,0), **B** =
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(xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So there are 9 parameters in
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total. The restricted form of edge vectors requires that **A** is
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along the x-axis, **B** is in the xy plane with a y-component in
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the +y direction, and **C** has a z-component in the +z direction.
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Note that a restricted triclinic box is always *right-handed* so
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that (**A** x **B**) points in the direction of **C**.
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edge vectors are of the following restricted form: **A** =
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(xhi-xlo,0,0), **B** = (xy,yhi-ylo,0), **C** = (xz,yz,zhi-zlo). So
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there are 9 parameters in total. Note that the restricted form
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requires **A** to be along the x-axis, **B** to be in the xy plane
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with a y-component in the +y direction, and **C** to have its
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z-component in the +z direction. Note that a restricted triclinic box
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is *right-handed* by construction since (**A** cross **B**) points in
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the direction of **C**.
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The *xy,xz,yz* values can be zero or positive or negative. They are
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called "tilt factors" because they are the amount of displacement
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applied to edges of faces of an originally orthogonal box to change it
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into a restricted triclinic parallelepiped.
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applied to edges of faces of an orthogonal box to change it into a
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restricted triclinic parallelepiped.
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.. note::
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Any general triclinic box (i.e. solid-state crystal basis vectors)
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can be rotated in 3d around its origin (and reflected across a
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plane if necessary to flip from a left-handed coordinate system to
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right-handed) in order to conform to the LAMMPS definition of a
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restricted triclinic box. See the discussion in the next
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sub-section about general triclinic simulation boxes in LAMMPS.
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Any right-handed general triclinic box (i.e. solid-state crystal
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basis vectors) can be rotated in 3d around its origin in order to
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conform to the LAMMPS definition of a restricted triclinic box.
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See the discussion in the next sub-section about general triclinic
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simulation boxes in LAMMPS.
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Note that the :doc:`thermo_style custom <thermo_style>` command has
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keywords for outputting the various parameters that define both
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restricted and general triclinic simulation boxes. Thus you can check
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the restricted triclinic box parameters LAMMPS generates to
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rotate/reflect a general triclinic box to restricted triclinic form.
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the restricted triclinic box parameters LAMMPS generates to rotate a
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general triclinic box to restricted triclinic form.
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For restricted triclinic boxes there are 9 thermo keywords for
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For restricted triclinic boxes these are the 9 thermo keywords for
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(xlo,ylo,zlo), (xhi,yhi,zhi), and the (xy,xz,yz) tilt factors. For
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general triclinic boxes there are 12 thermo keywords for (xlo,ylo,zhi)
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and the components of the **A**, **B**, **C** edge vectors. For both
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orthogonal and restricted triclinic boxes, the thermo keywords
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lx/ly/lz refer to the box sizes, namely lx = xhi - xlo, etc.
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general triclinic boxes these are the 12 thermo keywords for
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(xlo,ylo,zhi) and the components of the **A**, **B**, **C** edge
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vectors. For both orthogonal and restricted triclinic boxes, the
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thermo keywords lx/ly/lz refer to the box sizes, namely lx = xhi -
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xlo, etc. Lx,ly,lz are the box edge vector lengths for orthogonal and
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restricted/general triclinic simulation boxes.
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The remainder of this doc page explains (a) how LAMMPS operates with
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general triclinic simulation boxes, (b) mathematical transformations
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@ -124,7 +127,7 @@ input to LAMMPS. Likewise it allows output of dump files, data files,
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and thermodynamic data (e.g. pressure tensor) in a general triclinic
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format.
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However, internally, LAMMPS only uses restricted triclinic simulation
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However internally, LAMMPS only uses restricted triclinic simulation
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boxes. This is for parallel efficiency and to formulate partitioning
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of the simulation box across processors, neighbor list building, and
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inter-processor communication of per-atom data with methods similar to
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@ -139,31 +142,39 @@ This means 4 things which are important to understand:
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conversion from a restricted to general triclinic system is done at
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the time of output.
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* The conversion of the simulation box and per-atom data from general
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triclinic to restriced triclinic (and vice versa) is a rotation +
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optional reflection from one set of coordinate axes to another. For
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orthogonal and restricted triclinic systems, the coordinate axes are
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the standard x,y,z axes. For a general triclinic system, those
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coordinate axes are rotated in 3d. The optional reflection flips
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the axes from right-handed to left-handed if necessary. The 3
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rotated/reflected axes remain mutually orthogonal. For all 3 kinds
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of systems (orthogonal, restricted, general), per-atom quantities
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(e.g. coords, velocities) are input/output as values consistent with
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the corresponding coordinate axes.
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* Other LAMMPS commands such as the :doc:`boundary <boundary>` or
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:doc:`region <region>` or :doc:`velocity <velocity>` or :doc:`set
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<set>` commands, operate on restricted triclinic systems even if a
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general triclinic system was defined initially. For an example, see
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the paragraph below the folliowing list.
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triclinic to restricted triclinic (and vice versa) is a 3d rotation
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operation around an origin, which is the lower left corner of the
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simulation box. This means an input data file for a general
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triclinic system should specify all per-atom quantities consistent
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with the general triclinic box and its orientation relative to the
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standard x,y,z coordinate axes. For example, atom coordinates
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should be inside the general triclinic simulation box defined by the
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edge vectors **A**, **B**, **C** and its origin. Likewise per-atom
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velocities should be in directions consistent with the general
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triclinic box orientation. I.e. a velocity vector that will be in
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the +x direction once LAMMPS converts from a general to restricted
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triclinic box, should be specified in the data file in the direction
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of the **A** edge vector. See the :doc:`read_data <read_data>` doc
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page for info on all the per-atom vector quantities this rule
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affects when the data file for a general triclinic box is input.
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* If commands such as :doc:`write_data <write_data>` or :doc:`dump
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custom <dump>` are used to output general triclinic information, it
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is effectively the inverse of the operation described in the
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preceeding bullet.
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* Other LAMMPS commands such as :doc:`region <region>` or
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:doc:`velocity <velocity>` or :doc:`set <set>`, operate on a
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restricted triclinic system even if a general triclinic system was
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defined initially.
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This is the list of commands which have general triclinic options:
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* :doc:`create_box <create_box>` - define a general triclinic box
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* :doc:`create_atoms <create_atoms>` - add atoms to a general triclinic box
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* :doc:`lattice <lattice>` - define a custom lattice consistent with **A**, **B**, **C** edge vectors of a general triclinic box
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* :doc:`lattice <lattice>` - define a custom lattice consistent with the **A**, **B**, **C** edge vectors of a general triclinic box
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* :doc:`read_data <read_data>` - read a data file for a general triclinic system
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* :doc:`write_data <write_data>` - write a data file for a general triclinic system
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* :doc:`dump atom, dump custom <dump>` - output dump snapshots in general triclinic format
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* :doc:`dump_modify <dump_modify>` - switch a dump file between restrictied and general triclinic format
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* :doc:`dump_modify <dump_modify>` - toggle a dump file between restrictied and general triclinic format
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* :doc:`thermo_style <thermo_style>` - output the pressure tensor in
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general triclinic format
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* :doc:`thermo_modify <thermo_modify>` - toggle thermo-style output
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@ -171,42 +182,15 @@ This is the list of commands which have general triclinic options:
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* :doc:`read_restart <read_restart>` - read a restart file for a general tricliinc system
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* :doc:`write_restart <read_restart>` - write a restart file for a general tricliinc system
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As an example, consider the velocity of each atom in a general
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triclinic system. In a general triclinic data file, each atom will
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have coordinates inside a general triclinic box with arbitrary edge
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vectors **A**, **B**, **C**. If the file has a "Velocities" section
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then the velocity vector of each atom should be in a direction
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consistent with the orientation of the general triclnic coordinate
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axes.
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When LAMMPS internally converts the general triclinic system to
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restricted triclinic, the coordinates of all atoms are transformed
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(rotation + optional reflection) to be inside the new restricted
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triclinic box. Likewise the velocity vectors are transformed.
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If the :doc:`velocity <velocity>` command is used to set an x-velocity
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component, it will use the coordinate axes of the restricted box.
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If the atoms and their velocities are output via the :doc:`write_data
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<write_data>` or :doc:`dump custom <dump>` commands, the coordinates
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will be transformed (inverse rotation + optional reflection) to be
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inside the general triclinic box. Likewise the velocity vector for
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each atom will be transformed from restricted to general triclinic.
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Any other vector quantities associated with atoms (magnetic moments,
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spins, etc) are transformed in a similar manner back-and-forth between
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general and restricted box orientations.
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----------
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Transformation from general to restricted triclinic boxes
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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Let **A**,\ **B**,\ **C** be the edge vectors of a general triclinic
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simulation box. Assume that **A** x **B** . **C** > 0. The
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equivalent LAMMPS **a**,\ **b**,\ **c** for a restricted triclinic box
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are a linear rotation of **A**, **B**, and **C** and can be computed
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as follows:
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Let **A**,\ **B**,\ **C** be the right-handed edge vectors of a
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general triclinic simulation box. The equivalent LAMMPS **a**,\
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**b**,\ **c** for a restricted triclinic box are a 3d rotation of
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**A**, **B**, and **C** and can be computed as follows:
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.. math::
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@ -228,15 +212,10 @@ symbol (\^) indicates the corresponding unit vector. :math:`\beta` and
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:math:`\gamma` are angles between the **A**, **B**, **C** vectors
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as described below.
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If **A** x **B** . **C** < 0 the above equations are not valid for
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**c**\ . In this case, it is necessary to first apply an
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inversion. This can be achieved by interchanging two of the **A**,
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**B**, **C** vectors or by changing the sign of one of them.
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For consistency, the same rotation/inversion applied to the triclinic
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box edge vectors can also be applied to atom positions, velocities,
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and other vector quantities. This can be conveniently achieved by
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first converting to fractional coordinates in the general triclinic
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For consistency, the same rotation applied to the triclinic box edge
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vectors can also be applied to atom positions, velocities, and other
|
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vector quantities. This can be conveniently achieved by first
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converting to fractional coordinates in the general triclinic
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coordinates and then converting to coordinates in the resetricted
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triclinic basis. The transformation is given by the following
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equation:
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@ -335,9 +314,9 @@ Periodicity and tilt factors for triclinic simulation boxes
|
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
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|
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There is no requirement that a triclinic box be periodic in any
|
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dimension, though it typically should be in y or z if you wish enforce
|
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a shift in coordinates due to periodic boundary conditions across the
|
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y or z boundaries. See the doc page for the :doc:`boundary
|
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dimension, though it typically should be in y or z if you wish to
|
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enforce a shift in coordinates due to periodic boundary conditions
|
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across the y or z boundaries. See the doc page for the :doc:`boundary
|
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<boundary>` command for an explanation of shifted coordinates for
|
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restricted triclinic boxes which are periodic.
|
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|
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@ -83,10 +83,10 @@ See the :doc:`Howto triclinic <Howto_triclinic>` page for a
|
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description of both general and restricted triclinic boxes and how to
|
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define them. General triclinic boxes (arbitrary edge vectors **A**,
|
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**B**, and **C**) are converted internally to restricted triclinic
|
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boxes with tilt factors (xy,xz,yz) added to skew an otherwise
|
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orthogonal box.
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boxes with tilt factors (xy,xz,yz) which skew an otherwise orthogonal
|
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box.
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|
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The boundary <boundary> command settings expalined above for the 6
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The boundary <boundary> command settings explained above for the 6
|
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faces of an orthogonal box also apply in similar manner to the 6 faces
|
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of a restricted triclinix box (and thus to the corresponding 6 faces
|
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of a general triclinic box), with the following context.
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@ -1038,7 +1038,7 @@ void Atom::deallocate_topology()
|
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|
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/* ----------------------------------------------------------------------
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unpack N lines from Atom section of data file
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call style-specific routine to parse line
|
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call atom-style specific method to parse each line
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triclinic_general = 1 if data file defines a general triclinic box
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------------------------------------------------------------------------- */
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@ -1217,6 +1217,8 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
|
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
|
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
|
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// atom-style specific method parses single line
|
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avec->data_atom(xdata,imagedata,values,typestr);
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typestr = utils::utf8_subst(typestr);
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@ -1659,7 +1659,6 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vector<std:
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{
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int m, n, datatype, cols;
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void *pdata;
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double vector[3];
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int nlocal = atom->nlocal;
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if (nlocal == nmax) grow(0);
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@ -2227,7 +2226,8 @@ void AtomVec::write_improper(FILE *fp, int n, tagint **buf, int index)
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/* ----------------------------------------------------------------------
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convert info input by read_data from general to restricted triclinic
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parent class only operates on data from Velocities section of data file
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atom coords are converted in Atom::data_atoms()
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parent class operates on data from Velocities section of data file
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child classes operate on all other data: Atoms, Ellipsoids, Lines, Triangles, etc
|
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------------------------------------------------------------------------- */
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@ -2256,6 +2256,7 @@ void AtomVec::read_data_general_to_restricted(int nlocal_previous, int nlocal)
|
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|
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/* ----------------------------------------------------------------------
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convert info output by write_data from restricted to general triclinic
|
||||
create "hold" copy of original restricted data to restore after data file is written
|
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parent class only operates on x and data from Velocities section of data file
|
||||
child classes operate on all other data: Atoms, Ellipsoids, Lines, Triangles, etc
|
||||
------------------------------------------------------------------------- */
|
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@ -292,12 +292,13 @@ void Domain::set_global_box()
|
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}
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|
||||
// update general triclinic box if defined
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||||
// reset ABC edge vectors from restricted triclinic box
|
||||
// boxlo = lower left corner of general triclinic box
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||||
// reset general tri ABC edge vectors from restricted tri box
|
||||
|
||||
if (triclinic_general) {
|
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double aprime[3],bprime[3],cprime[3];
|
||||
|
||||
// A'B'C' = edge vectors of restricted triclinic box
|
||||
|
||||
aprime[0] = boxhi[0] - boxlo[0];
|
||||
aprime[1] = aprime[2] = 0.0;
|
||||
bprime[0] = xy;
|
||||
|
||||
@ -40,7 +40,7 @@ class Domain : protected Pointers {
|
||||
// 3 = shrink-wrap non-per w/ min
|
||||
|
||||
int triclinic; // 0 = orthog box, 1 = triclinic (restricted or general)
|
||||
int triclinic_general; // 1 if mapping to/from general triclinic is stored, 0 if not
|
||||
int triclinic_general; // 1 if general <-> restricted tri mapping is stored, 0 if not
|
||||
|
||||
// orthogonal box
|
||||
|
||||
@ -50,7 +50,7 @@ class Domain : protected Pointers {
|
||||
double prd_half[3]; // array form of half dimensions
|
||||
|
||||
// restricted triclinic box
|
||||
// xyzprd,xyzprd_half and prd,prd_half = same as if not tilted
|
||||
// xyz prd,xyz prd_half and prd,prd_half = same as if not tilted
|
||||
|
||||
double prd_lamda[3]; // lamda box = (1,1,1)
|
||||
double prd_half_lamda[3]; // lamda half box = (0.5,0.5,0.5)
|
||||
|
||||
@ -576,7 +576,7 @@ void ReadData::command(int narg, char **arg)
|
||||
|
||||
if (!triclinic_general) {
|
||||
|
||||
// orthongal box
|
||||
// orthogonal or restricted triclinic box
|
||||
|
||||
domain->boxlo[0] = boxlo[0];
|
||||
domain->boxhi[0] = boxhi[0];
|
||||
@ -605,8 +605,6 @@ void ReadData::command(int narg, char **arg)
|
||||
|
||||
// change simulation box to be union of existing box and new box + shift
|
||||
// only done if firstpass and not first data file
|
||||
// for restricted triclinic, new tilt factors not allowed
|
||||
// for general triclinic, different new box and shift not allowed
|
||||
|
||||
if (firstpass && addflag != NONE) {
|
||||
|
||||
@ -670,7 +668,7 @@ void ReadData::command(int narg, char **arg)
|
||||
int flag_all;
|
||||
MPI_Allreduce(&iflag, &flag_all, 1, MPI_INT, MPI_SUM, world);
|
||||
if ((flag_all > 0) && (comm->me == 0))
|
||||
error->warning(FLERR, "Non-zero image flags with growing box leads to bad coordinates");
|
||||
error->warning(FLERR, "Non-zero image flags with growing box can produce bad coordinates");
|
||||
}
|
||||
}
|
||||
|
||||
@ -689,6 +687,7 @@ void ReadData::command(int narg, char **arg)
|
||||
lmap = new LabelMap(lmp, ntypes, nbondtypes, nangletypes, ndihedraltypes, nimpropertypes);
|
||||
}
|
||||
|
||||
// -------------------------------------------------------------------------------------
|
||||
// rest of data file is Sections
|
||||
// read in any order, except where error checks
|
||||
// customize for new sections
|
||||
@ -1391,10 +1390,9 @@ void ReadData::header(int firstpass)
|
||||
if (addflag == NONE) atom->nimpropertypes = nimpropertypes + extra_improper_types;
|
||||
|
||||
// these settings only used by first data file
|
||||
// also, these are obsolescent. we parse them to maintain backward
|
||||
// compatibility, but the recommended way is to set them via keywords
|
||||
// in the LAMMPS input file. In case these flags are set in both,
|
||||
// the input and the data file, we use the larger of the two.
|
||||
// NOTEL these are now obsolete, we parse them to maintain backward compatibility
|
||||
// the recommended way is to set them via command keywords in the input script
|
||||
// if these flags are set both ways, the larger of the two values is used
|
||||
|
||||
} else if (strstr(line, "extra bond per atom")) {
|
||||
if (addflag == NONE) extra_flag_value = utils::inumeric(FLERR, words[0], false, lmp);
|
||||
|
||||
@ -59,15 +59,16 @@ class ReadData : public Command {
|
||||
|
||||
class LabelMap *lmap;
|
||||
|
||||
// box info
|
||||
// box info read from file
|
||||
|
||||
int triclinic, triclinic_general;
|
||||
int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag;
|
||||
int avec_flag, bvec_flag, cvec_flag, abc_origin_flag;
|
||||
|
||||
double boxlo[3], boxhi[3];
|
||||
double xy, xz, yz;
|
||||
double avec[3], bvec[3], cvec[3];
|
||||
double abc_origin[3];
|
||||
int triclinic, triclinic_general;
|
||||
int xloxhi_flag, yloyhi_flag, zlozhi_flag, tilt_flag;
|
||||
int avec_flag, bvec_flag, cvec_flag, abc_origin_flag;
|
||||
|
||||
// optional args
|
||||
|
||||
|
||||
Reference in New Issue
Block a user