Merge pull request brucefan1983#1336 from brucefan1983/rdf_speedup

RDF generalization and speedup

Author: yongwangxx

doc/gpumd/input_parameters/compute_rdf.rst

@@ -33,18 +33,13 @@ Syntax
 
 This keyword is used as follows::
 
-  compute_rdf <cutoff> <num_bins> <interval> [atom <i1> <i2> atom <i3> <i4> ...]
+  compute_rdf <cutoff> <num_bins> <interval> 
 
 This means that the :term:`RDF` calculations will be performed every :attr:`interval` steps, with :attr:`num_bins` data points evenly distributed from 0 to :attr:`cutoff` (in units of Ångstrom) in terms of the distance between atom pairs.
 
-Without the optional parameters, only the total :term:`RDF` will be calculated.
-
-To additionally calculate the partial :term:`RDF` for a pair of species, one can specify the types of the two species after the word "atom". 
-The types 0, 1, 2, ... correspond to the species in the potential file in order. 
-Currently, one can specify at most 6 pairs. 
+Starting from GPUMD-v4.9, there is no need to specify the atom pairs and the code will calculate the partial :term:`RDF`s for all atom pairs.
 
 Example
 -------
 
-   compute_rdf 8.0 400 1000 # total RDF every 1000 MD steps with 400 data up to 8 Angstrom
-   compute_rdf 8.0 400 1000 atom 0 0 atom 1 1 atom 0 1 # additionally calculate 3 partial RDFs
+   compute_rdf 8.0 400 1000 # Calculate all RDFs every 1000 MD steps with 400 data up to 8 Angstrom

src/main_gpumd/run.cu

@@ -514,7 +514,7 @@ void Run::parse_one_keyword(std::vector<std::string>& tokens)
     measure.properties.emplace_back(std::move(property));
   } else if (strcmp(param[0], "compute_rdf") == 0) {
     std::unique_ptr<Property> property;
-    property.reset(new RDF(param, num_param, box, number_of_types, number_of_steps));
+    property.reset(new RDF(param, num_param, box, atom.cpu_type_size, number_of_steps));
     measure.properties.emplace_back(std::move(property));
   } else if (strcmp(param[0], "compute_adf") == 0) {
     std::unique_ptr<Property> property;