CANDELA is short for Collection of ANalysis DEsigned for Large-scale Atomic simulations. It is developed by MCresearch to conduct analyses on MD trajectory in different formats. Right now the program only supports analysis of pair distribution function (PDF), static structure factor (SSF) and mean square displacement (MSD). The minimum supported version of ABACUS is 3.2.0.
Requirements for using CANDELA
For Detailed usage of CANDELA, please refer to the official document. There are two things which need special attention in using CANDELA with ABACUS. First, the input file of CANDELA only takes the name of
INPUT, the same as ABACUS input file, so you should not run CANDELA in the same folder where you run ABACUS. Second, to use CANDELA to postprocess ABACUS MD trajectory, the following parameters have to be specified in the
INPUT file of CANDELA in addition to other required parameters:
geo_in_typehas to be set to
msd_dthas to be specified in unit of picosecond, especially in the case of
geo_directoryhas to be set to the path to the
MD_dumpfile in the
OUT.xxxfolder. As a result, a CANDELA
INPUTfile for calculating PDF from ABACUS should be something like this:
calculation pdf # Pair Distribution Function. system Al geo_in_type LAMMPS geo_directory ../geo/Al64.dump geo_1 0 geo_2 20 geo_interval 1 geo_ignore 4 geo_out pdf.txt # output pdf name. ntype 1 # number of different types of atoms. natom 64 # total number of atoms. natom1 64 rcut 6 dr 0.01 # delta r in real space struf_dgx 0.05 struf_ng 200
More examples of CANDELA
INPUT with ABACUS can be found in the test directory.