Source Code for Module lib.structure.mass

 1  ############################################################################### 
 2  #                                                                             # 
 3  # Copyright (C) 2003-2013 Edward d'Auvergne                                   # 
 4  #                                                                             # 
 5  # This file is part of the program relax (http://www.nmr-relax.com).          # 
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 7  # This program is free software: you can redistribute it and/or modify        # 
 8  # it under the terms of the GNU General Public License as published by        # 
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15  # GNU General Public License for more details.                                # 
16  #                                                                             # 
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18  # along with this program.  If not, see <http://www.gnu.org/licenses/>.       # 
19  #                                                                             # 
20  ############################################################################### 
21   
22  # Python module imports. 
23  from numpy import float64, zeros 
24  from warnings import warn 
25   
26  # relax module imports. 
27  from lib.physical_constants import return_atomic_mass 
28  from lib.errors import RelaxError 
29  from lib.warnings import RelaxWarning 
30   
31   
32   
33 -def centre_of_mass(pos=None, elements=None, verbosity=1): 
34      """Calculate and return the centre of mass for the given atomic coordinates. 
35   
36      @keyword pos:           The list of atomic coordinates. 
37      @type pos:              list of lists of float 
38      @keyword elements:      The list of elements corresponding to the atoms. 
39      @type elements:         list of str 
40      @keyword verbosity:     The amount of text to print out.  0 results in no printouts, 1 the full amount. 
41      @type verbosity:        int 
42      @return:                The centre of mass vector and the mass. 
43      @rtype:                 3D list of floats, float 
44      """ 
45   
46      # Print out. 
47      if verbosity: 
48          print("Calculating the centre of mass.") 
49   
50      # Initialise the centre of mass. 
51      R = zeros(3, float64) 
52   
53      # Initialise the total mass. 
54      M = 0.0 
55   
56      # Loop over all atoms. 
57      for i in range(len(pos)): 
58          # Atomic mass. 
59          try: 
60              mass = return_atomic_mass(elements[i]) 
61          except RelaxError: 
62              warn(RelaxWarning("Skipping the atom index %s as the element '%s' is unknown." % (i, elements[i]))) 
63   
64          # Total mass. 
65          M = M + mass 
66   
67          # Sum of mass * position. 
68          R = R + mass * pos[i] 
69   
70      # Normalise. 
71      R = R / M 
72   
73      # Final printout. 
74      if verbosity: 
75          print("    Total mass:      M = " + repr(M)) 
76          print("    Centre of mass:  R = " + repr(R)) 
77   
78      # Return the centre of mass and total mass 
79      return R, M 
80