doc pages 949-1220
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@ -433,7 +433,7 @@ from owned to ghost cells, or ghost to owned cells, respectively, as
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described above. The *caller* argument should be one of these values
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-- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
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depending on the style of the caller class. The *ptr* argument is the
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"this" pointer to the caller class. These 2 arguments are used to
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"this" pointer to the caller class. These two arguments are used to
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call back to pack()/unpack() functions in the caller class, as
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explained below.
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@ -419,7 +419,7 @@ showing the use of the *template* atom style versus *molecular*.
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<molecule>` that contains multiple molecules, you should ensure the
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atom types, bond types, angle_types, etc in all the molecules are
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consistent. E.g. if one molecule represents H2O and another CO2,
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then you probably do not want each molecule file to define 2 atom
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then you probably do not want each molecule file to define two atom
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types and a single bond type, because they will conflict with each
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other when a mixture system of H2O and CO2 molecules is defined,
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e.g. by the :doc:`read_data <read_data>` command. Rather the H2O
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@ -59,10 +59,10 @@ coefficients need to be re-specified.
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When both a bond and pair style is defined, the
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:doc:`special_bonds <special_bonds>` command often needs to be used to
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turn off (or weight) the pairwise interaction that would otherwise
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exist between 2 bonded atoms.
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exist between two bonded atoms.
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In the formulas listed for each bond style, *r* is the distance
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between the 2 atoms in the bond.
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between the two atoms in the bond.
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----------
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@ -15,7 +15,7 @@ Syntax
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* inner,outer = inner and outer bond length (distance units)
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* file = name of file to write values to
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* keyword = section name in file for this set of tabulated values
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* itype,jtype = 2 atom types (optional)
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* itype,jtype = two atom types (optional)
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Examples
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""""""""
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@ -39,7 +39,7 @@ of the file to allow multiple tables of energy and force to be included
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in one file. The individual sections may be identified by the *keyword*.
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The energy and force values are computed at distances from *inner* to
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*outer* for 2 interacting atoms forming a bond of type *btype*, using
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*outer* for two interacting atoms forming a bond of type *btype*, using
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the appropriate :doc:`bond_coeff <bond_coeff>` coefficients. N evenly
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spaced distances are used.
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@ -36,7 +36,8 @@ script variables except for *atomfile* style variables (:doc:`variable
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Restrictions
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""""""""""""
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none
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none
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Related commands
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""""""""""""""""
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@ -55,7 +55,7 @@ commands. The decomposition can be changed via the
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Restrictions
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""""""""""""
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None
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none
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Related commands
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""""""""""""""""
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@ -362,7 +362,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
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Restrictions
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""""""""""""
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none
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none
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Related commands
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""""""""""""""""
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@ -73,7 +73,7 @@ keyword discussion below.
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For style *overlap* pairs of atoms whose distance of separation is
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within the specified cutoff distance are searched for, and one of the
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2 atoms is deleted. Only pairs where one of the two atoms is in the
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two atoms is deleted. Only pairs where one of the two atoms is in the
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first group specified and the other atom is in the second group are
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considered. The atom that is in the first group is the one that is
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deleted.
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@ -389,7 +389,7 @@ cylinders with that diameter, e.g. 1.0, which is in whatever distance
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If *atom* is specified for the *width* value, then each bond
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will be drawn with a width corresponding to the minimum diameter
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of the 2 atoms in the bond.
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of the two atoms in the bond.
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If *type* is specified for the *width* value then the diameter of each
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bond is determined by its bond type. By default all types have
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@ -206,7 +206,8 @@ FALSE.
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Restrictions
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""""""""""""
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none
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none
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Related commands
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""""""""""""""""
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@ -76,7 +76,6 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
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* :doc:`none <improper_none>` - turn off improper interactions
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* :doc:`zero <improper_zero>` - topology but no interactions
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* :doc:`hybrid <improper_hybrid>` - define multiple styles of improper interactions
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* :doc:`amoeba <improper_amoeba>` - AMOEBA out-of-plane improper
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* :doc:`class2 <improper_class2>` - COMPASS (class 2) improper
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* :doc:`cossq <improper_cossq>` - improper with a cosine squared term
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@ -88,8 +87,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
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* :doc:`inversion/harmonic <improper_inversion_harmonic>` - harmonic improper with Wilson-Decius out-of-plane definition
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* :doc:`ring <improper_ring>` - improper which prevents planar conformations
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* :doc:`umbrella <improper_umbrella>` - DREIDING improper
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:doc:`sqdistharm <improper_sqdistharm>` - improper that is harmonic in the square of the out-of-plane distance
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* :doc:`sqdistharm <improper_sqdistharm>` - improper that is harmonic in the square of the out-of-plane distance
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----------
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@ -35,7 +35,8 @@ scripts.
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Restrictions
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""""""""""""
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none
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none
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Related commands
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""""""""""""""""
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@ -130,7 +130,8 @@ process that writes output (usually MPI rank 0).
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Restrictions
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""""""""""""
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none
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none
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Related commands
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""""""""""""""""
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@ -428,7 +428,7 @@ Syntax
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* variable(s) = single name or list of names of (string style) LAMMPS
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variable(s) where a query result or parameter get result is stored. Variables
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that do not exist will be created by the command
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* formatarg = *list, split, or index* (optional):
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* formatarg = *list* or *split* or *index* (optional)
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.. parsed-literal::
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@ -697,17 +697,18 @@ Syntax
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* variable(s) = single name or list of names of (string style) LAMMPS
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variable(s) where a query result or parameter get result is stored. Variables
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that do not exist will be created by the command
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* formatarg = *list, split, or explicit* (optional):
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* formatarg = *list* or *split* or *explicit* (optional)
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.. parsed-literal::
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*list* = returns a single string with a list of space separated values
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(e.g. "1.0 2.0 3.0"), which is placed in a LAMMPS variable as
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defined by the *variable* argument.
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defined by the *variable* argument
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*split* = returns the values separately in new variables with names based
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on the prefix specified in *variable* and a number appended to
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indicate which element in the list of values is in the variable
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*explicit* = returns the values separately in one more more variable names
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provided as arguments that precede *formatarg*\ . [default]
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provided as arguments that precede *formatarg* (default)
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* values = new value(s) to replace the current value(s) of a KIM portable model
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parameter
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@ -459,7 +459,7 @@ The option defaults are as follows:
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* diff = ik (PPPM)
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* disp/auto = no
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* fftbench = no (PPPM)
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* force = -1.0,
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* force = -1.0
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* force/disp/kspace = -1.0
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* force/disp/real = -1.0
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* gewald = gewald/disp = 0.0
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@ -39,7 +39,8 @@ name of the initial log file can also be set by the :doc:`-log command-line swit
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Restrictions
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""""""""""""
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none
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none
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Related commands
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""""""""""""""""
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