# Run with the command: # moltemplate.sh -atomstyle "atomid atomtype flag density x y z" benzene_sample01.lt -allow-wildcards -nocheck import "benzene_cg.lt" # Specify the periodic boundary conditions: write_once("Data Boundary") { 0 35.0 xlo xhi 0 35.0 ylo yhi 0 35.0 zlo zhi } bulk = new BENZ [5].move(7, 0, 0) [5].move(0, 7, 0).rot(10,0,1,0) [5].move(0, 0, 7) # NOTE: # I included a .rot() rotation command above in order to demonstrate # that moltemplate can control ellipsoid orientation as well as position. # Unfortunately, this example may be difficult to understand. Explanation: # When ".rot(10,0,1,0)" appears in the middle of a 3-D array declaration, # it applies a rotation of 10 degrees around the y axis ("0,1,0") each time # the middle index ("j" in "BENZ[i][j][k]") increases by one. # This will cause the k-columns to be twisted around the y axis as y increases.