diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 29eea87e64..7eaf1081f3 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -322,27 +322,31 @@ all types from 1 to :math:`N`. A leading asterisk means all types from If :doc:`bond_style hybrid ` is used, *bstyle* should be a sub-style name. The bond styles that currently work with fix adapt are: -+-----------------------------------------------------+------------+------------+ -| :doc:`class2 ` | r0 | type bonds | -+-----------------------------------------------------+------------+------------+ -| :doc:`fene ` | k,r0 | type bonds | -+-----------------------------------------------------+------------+------------+ -| :doc:`fene/nm ` | k,r0 | type bonds | -+-----------------------------------------------------+------------+------------+ -| :doc:`gromos ` | k,r0 | type bonds | -+-----------------------------------------------------+------------+------------+ -| :doc:`harmonic ` | k,r0 | type bonds | -+-----------------------------------------------------+------------+------------+ -| :doc:`harmonic/shift ` | k,r0,r1 | type bonds | -+-----------------------------------------------------+------------+------------+ -| :doc:`harmonic/shift/cut ` | k,r0,r1 | type bonds | -+-----------------------------------------------------+------------+------------+ -| :doc:`harmonic/restrain ` | k | type bonds | -+-----------------------------------------------------+------------+------------+ -| :doc:`morse ` | r0 | type bonds | -+-----------------------------------------------------+------------+------------+ -| :doc:`nonlinear ` | epsilon,r0 | type bonds | -+-----------------------------------------------------+------------+------------+ ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`class2 ` | r0 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`fene ` | k,r0 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`fene/expand ` | k,r0,epsilon,sigma,shift | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`fene/nm ` | k,r0 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`gromos ` | k,r0 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`harmonic ` | k,r0 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`harmonic/restrain ` | k | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`harmonic/shift ` | k,r0,r1 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`harmonic/shift/cut ` | k,r0,r1 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`mm3 ` | k,r0 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`morse ` | r0 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ +| :doc:`nonlinear ` | epsilon,r0 | type bonds | ++-----------------------------------------------------+---------------------------+------------+ ---------- @@ -365,13 +369,31 @@ all types from 1 to :math:`N`. A leading asterisk means all types from If :doc:`angle_style hybrid ` is used, *astyle* should be a sub-style name. The angle styles that currently work with fix adapt are: -+-----------------------------------------------+----------+-------------+ -| :doc:`harmonic ` | k,theta0 | type angles | -+-----------------------------------------------+----------+-------------+ -| :doc:`cosine ` | k | type angles | -+-----------------------------------------------+----------+-------------+ -| :doc:`cosine/squared ` | k,theta0 | type angles | -+-----------------------------------------------+----------+-------------+ ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`harmonic ` | k,theta0 | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`charmm ` | k,theta0 | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`class2 ` | k2,k3,k4,theta0 | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`cosine ` | k | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`cosine/periodic ` | k,b,n | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`cosine/squared/restricted ` | k,theta0 | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`dipole ` | k,gamma0 | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`fourier ` | k,c0,c1,c2 | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`fourier/simple ` | k,c,n | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`mm3 ` | k,theta0 | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`quartic ` | k2,k3,k4,theta0 | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ +| :doc:`spica ` | k,theta0 | type angles | ++--------------------------------------------------------------------+-----------------+-------------+ Note that internally, theta0 is stored in radians, so the variable this fix uses to reset theta0 needs to generate values in radians. diff --git a/doc/src/read_dump.rst b/doc/src/read_dump.rst index f912390b10..a803feb65e 100644 --- a/doc/src/read_dump.rst +++ b/doc/src/read_dump.rst @@ -115,10 +115,11 @@ to tell LAMMPS how many parallel files exist, via its specified The format of the dump file is selected through the *format* keyword. If specified, it must be the last keyword used, since all remaining -arguments are passed on to the dump reader. The *native* format is -for native LAMMPS dump files, written with a :doc:`dump atom ` -or :doc:`dump custom ` command. The *xyz* format is for generic XYZ -formatted dump files. These formats take no additional values. +arguments are passed on to the dump reader. The *native* format is for +native LAMMPS dump files, written with a :doc:`dump atom ` or +:doc:`dump custom ` command. The *xyz* format is for generic XYZ +formatted dump files (see details below). These formats take no +additional values. The *molfile* format supports reading data through using the `VMD `_ molfile plugin interface. This dump reader format is only available, @@ -231,17 +232,26 @@ will then have a label corresponding to the fix-ID rather than "x" or labels for fields *id* and *type*\ . For dump files in *xyz* format, only the *type*, *x*, *y*, and *z* -fields are supported. If the atoms have an integer number as label -(like when they are created with default setting by :doc:`dump style -` *xyz*), that number will be used at atom type. The the atom -label is a string, it is required that a map is created using the -:doc:`labelmap command ` that maps those labels to the -(numeric) atom types that LAMMPS uses. The xyz format dump file does -not store atom IDs, so these are assigned consecutively to the atoms as -they appear in the dump file, starting from 1. Thus you should ensure -that order of atoms is consistent from snapshot to snapshot in the XYZ -dump file. See the :doc:`dump_modify sort ` command if the -XYZ dump file was written by LAMMPS. +fields are supported. There are many variants of the XYZ file format. +LAMMPS will read the number of atoms from the first line of each frame, +ignore the second (title) line, and then read one line for each atom in the format: + +.. parsed-literal:: + +