This is part III of a se­ries of three posts about op­ti­miz­ing python code. The par­tic­u­lar ex­am­ple given is the com­pu­ta­tion of pair-wise dis­tances un­der pe­ri­odic bound­ary con­di­tion which is an es­sen­tial part of mol­e­c­u­lar dy­nam­ics sim­u­la­tions. In this post, I show how to use Numpy to do the com­pu­ta­tion.

This is part II of a se­ries of three posts about op­ti­miz­ing python code. The par­tic­u­lar ex­am­ple given is the com­pu­ta­tion of pair-wise dis­tances un­der pe­ri­odic bound­ary con­di­tion which is an es­sen­tial part of mol­e­c­u­lar dy­nam­ics sim­u­la­tions. In this post, I show how to use Numpy to do the com­pu­ta­tion.

In this se­ries of posts, us­ing cal­cu­la­tion of pair-wise dis­tances un­der pe­ri­odic bound­ary con­di­tion as an ex­am­ple, I show sev­eral dif­fer­ent meth­ods to op­ti­mize Python codes. The per­for­mances from dif­fer­ent meth­ods are bench­marked for com­par­i­son.