Source Code for Module lib.structure.mass

 1  ############################################################################### 
 2  #                                                                             # 
 3  # Copyright (C) 2003-2008,2012-2013 Edward d'Auvergne                         # 
 4  # Copyright (C) 2008 Sebastien Morin                                          # 
 5  #                                                                             # 
 6  # This file is part of the program relax (http://www.nmr-relax.com).          # 
 7  #                                                                             # 
 8  # This program is free software: you can redistribute it and/or modify        # 
 9  # it under the terms of the GNU General Public License as published by        # 
10  # the Free Software Foundation, either version 3 of the License, or           # 
11  # (at your option) any later version.                                         # 
12  #                                                                             # 
13  # This program is distributed in the hope that it will be useful,             # 
14  # but WITHOUT ANY WARRANTY; without even the implied warranty of              # 
15  # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               # 
16  # GNU General Public License for more details.                                # 
17  #                                                                             # 
18  # You should have received a copy of the GNU General Public License           # 
19  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
20  #                                                                             # 
21  ############################################################################### 
22   
23  # Python module imports. 
24  from numpy import float64, zeros 
25  from warnings import warn 
26   
27  # relax module imports. 
28  from lib.periodic_table import periodic_table 
29  from lib.errors import RelaxError 
30  from lib.warnings import RelaxWarning 
31   
32   
33   
34 -def centre_of_mass(pos=None, elements=None, verbosity=1): 
35      """Calculate and return the centre of mass for the given atomic coordinates. 
36   
37      @keyword pos:           The list of atomic coordinates. 
38      @type pos:              list of lists of float 
39      @keyword elements:      The list of elements corresponding to the atoms. 
40      @type elements:         list of str 
41      @keyword verbosity:     The amount of text to print out.  0 results in no printouts, 1 the full amount. 
42      @type verbosity:        int 
43      @return:                The centre of mass vector and the mass. 
44      @rtype:                 3D list of floats, float 
45      """ 
46   
47      # Print out. 
48      if verbosity: 
49          print("Calculating the centre of mass.") 
50   
51      # Initialise the centre of mass. 
52      R = zeros(3, float64) 
53   
54      # Initialise the total mass. 
55      M = 0.0 
56   
57      # Loop over all atoms. 
58      for i in range(len(pos)): 
59          # Atomic mass. 
60          try: 
61              mass = periodic_table.atomic_mass(elements[i]) 
62          except RelaxError: 
63              warn(RelaxWarning("Skipping the atom index %s as the element '%s' is unknown." % (i, elements[i]))) 
64   
65          # Total mass. 
66          M = M + mass 
67   
68          # Sum of mass * position. 
69          R = R + mass * pos[i] 
70   
71      # Normalise. 
72      R = R / M 
73   
74      # Final printout. 
75      if verbosity: 
76          print("    Total mass:      M = " + repr(M)) 
77          print("    Centre of mass:  R = " + repr(R)) 
78   
79      # Return the centre of mass and total mass 
80      return R, M 
81