Pairwise distances are generated by looping over a pairwise neighbor list, just as they would be in a pair_style -computation. The distance between two atoms I and J is included in -a specific histogram if the following criteria are met: +computation. The distance between two atoms I and J is included in a +specific histogram if the following criteria are met:
A coordination number coord(r) is also calculated, which is the -number of atoms of type jtypeN within the current bin or closer, -averaged over atoms of type itypeN. This is calculated as the area- -or volume-weighted sum of g(r) values over all bins up to and including the -current bin, multiplied by the global average volume density of atoms of type -jtypeN. +
A coordination number coord(r) is also calculated, which is the number +of atoms of type jtypeN within the current bin or closer, averaged +over atoms of type itypeN. This is calculated as the area- or +volume-weighted sum of g(r) values over all bins up to and including +the current bin, multiplied by the global average volume density of +atoms of type jtypeN.
The simplest way to output the results of the compute rdf calculation to a file is to use the fix ave/time command, for @@ -125,15 +125,13 @@ since processors (in parallel) don't know about atom coordinates for atoms further away than that distance. If you want an RDF for larger distances, you can use the rerun command to post-process a dump file. The definition of g(r) used by LAMMPS is only appropriate -for characterizing atoms that are uniformly distributed -throughout the simulation cell. In such cases, -the coordination number is still correct and meaningful. -As an example, if a large simulation -cell contains only one atom of type itypeN and one of jtypeN, -then g(r) will register an arbitrarily large spike at whatever -distance they happen to be at, and zero everywhere else. -coord(r) will show a step change from zero to one at the location -of the spike in g(r). +for characterizing atoms that are uniformly distributed throughout the +simulation cell. In such cases, the coordination number is still +correct and meaningful. As an example, if a large simulation cell +contains only one atom of type itypeN and one of jtypeN, then g(r) +will register an arbitrarily large spike at whatever distance they +happen to be at, and zero everywhere else. coord(r) will show a step +change from zero to one at the location of the spike in g(r).
Related commands:
diff --git a/doc/compute_rdf.txt b/doc/compute_rdf.txt index 122bf7a2c7..00f3677cbf 100644 --- a/doc/compute_rdf.txt +++ b/doc/compute_rdf.txt @@ -63,8 +63,8 @@ types represented by {jtypeN} are the distribution atom. Pairwise distances are generated by looping over a pairwise neighbor list, just as they would be in a "pair_style"_pair_style.html -computation. The distance between two atoms I and J is included in -a specific histogram if the following criteria are met: +computation. The distance between two atoms I and J is included in a +specific histogram if the following criteria are met: atoms I,J are both in the specified compute group the distance between atoms I,J is less than the maximum force cutoff @@ -82,12 +82,12 @@ involves the count of {itypeN} atoms, the count of {jtypeN} atoms, the volume of the entire simulation box, and the volume of the bin's thin shell in 3d (or the area of the bin's thin ring in 2d). -A coordination number coord(r) is also calculated, which is the -number of atoms of type {jtypeN} within the current bin or closer, -averaged over atoms of type {itypeN}. This is calculated as the area- -or volume-weighted sum of g(r) values over all bins up to and including the -current bin, multiplied by the global average volume density of atoms of type -jtypeN. +A coordination number coord(r) is also calculated, which is the number +of atoms of type {jtypeN} within the current bin or closer, averaged +over atoms of type {itypeN}. This is calculated as the area- or +volume-weighted sum of g(r) values over all bins up to and including +the current bin, multiplied by the global average volume density of +atoms of type jtypeN. The simplest way to output the results of the compute rdf calculation to a file is to use the "fix ave/time"_fix_ave_time.html command, for @@ -122,15 +122,13 @@ since processors (in parallel) don't know about atom coordinates for atoms further away than that distance. If you want an RDF for larger distances, you can use the "rerun"_rerun.html command to post-process a dump file. The definition of g(r) used by LAMMPS is only appropriate -for characterizing atoms that are uniformly distributed -throughout the simulation cell. In such cases, -the coordination number is still correct and meaningful. -As an example, if a large simulation -cell contains only one atom of type {itypeN} and one of {jtypeN}, -then g(r) will register an arbitrarily large spike at whatever -distance they happen to be at, and zero everywhere else. -coord(r) will show a step change from zero to one at the location -of the spike in g(r). +for characterizing atoms that are uniformly distributed throughout the +simulation cell. In such cases, the coordination number is still +correct and meaningful. As an example, if a large simulation cell +contains only one atom of type {itypeN} and one of {jtypeN}, then g(r) +will register an arbitrarily large spike at whatever distance they +happen to be at, and zero everywhere else. coord(r) will show a step +change from zero to one at the location of the spike in g(r). [Related commands:]