Source Code for Module functions.d2ri

 1  from Numeric import copy 
 2   
 3 -class d2Ri: 
 4 -        def __init__(self): 
 5                  "An additional layer of equations to simplify the relaxation equations, gradients, and hessians." 
 6                   
 7   
 8   
 9 -        def d2Ri(self): 
10                  """An additional layer of equations to simplify the relaxation equations, gradients, and hessians. 
11   
12                  The R1 and R2 equations are left alone, while the NOE is decomposed into the cross relaxation rate equation and the R1 equation. 
13   
14   
15                  The relaxation hessians 
16                  ~~~~~~~~~~~~~~~~~~~~~~~ 
17   
18                  Data structure:  self.data.d2ri 
19                  Dimension:  3D, (parameters, parameters, relaxation data) 
20                  Type:  Numeric array, Float64 
21                  Dependencies:  self.data.ri_prime, self.data.dri_prime, self.data.d2ri_prime 
22                  Required by:  self.data.d2chi2 
23   
24   
25                  Formulae 
26                  ~~~~~~~~ 
27   
28                               d2R1()             d2R1'() 
29                          ---------------  =  --------------- 
30                          dthetaj.dthetak     dthetaj.dthetak 
31   
32   
33                               d2R2()             d2R2'() 
34                          ---------------  =  --------------- 
35                          dthetaj.dthetak     dthetaj.dthetak 
36   
37   
38                              d2NOE()         gH      1      /               /      dR1()     dR1()                  d2R1()     \  
39                          ---------------  =  -- . ------- . | sigma_noe() . | 2 . ------- . -------  -  R1() . --------------- | 
40                          dthetaj.dthetak     gN   R1()**3   \               \     dthetaj   dthetak            dthetaj.dthetak / 
41   
42                                            / dsigma_noe()    dR1()       dR1()    dsigma_noe()             d2sigma_noe()  \ \  
43                                  -  R1() . | ------------ . -------  +  ------- . ------------  -  R1() . --------------- | | 
44                                            \   dthetaj      dthetak     dthetaj     dthetak               dthetaj.dthetak / / 
45                  """ 
46   
47                  # Calculate the transformed relaxation hessians (the transformed relaxation values and gradients have been previously calculated by the d2Chi2 function). 
48                  self.d2Ri_prime() 
49   
50                  # Copy the relaxation hessians from self.data.d2ri_prime 
51                  self.data.d2ri = copy.deepcopy(self.data.d2ri_prime) 
52   
53                  # Loop over the relaxation values and modify the NOE hessians. 
54                  for i in range(self.mf.data.num_ri): 
55                          if self.mf.data.data_types[i] == 'NOE': 
56                                  r1_index = self.mf.data.noe_r1_table[i] 
57                                  r1 = self.data.ri_prime[r1_index] 
58                                  if r1 == None: 
59                                          raise NameError, "Incomplete code, need to somehow calculate the r1 value." 
60                                  for param1 in range(len(self.data.ri_param_types)): 
61                                          for param2 in range(param1 + 1): 
62                                                  if r1 == 0: 
63                                                          self.data.d2ri[param1, param2, i] = 1e99 
64                                                  else: 
65                                                          a = self.data.ri_prime[i] * (2.0 * self.data.dri_prime[param1, r1_index] * self.data.dri_prime[param2, r1_index] - r1 * self.data.d2ri_prime[param1, param2, r1_index]) 
66                                                          b = r1 * (self.data.dri_prime[param1, i] * self.data.dri_prime[param2, r1_index] + self.data.dri_prime[param1, i] * self.data.dri_prime[param2, r1_index] - r1 * self.data.d2ri_prime[param1, param2, i]) 
67                                                          self.data.d2ri[param1, param2, i] = (self.mf.data.gh/self.mf.data.gx) * (1.0 / r1**3) * (a - b) 
68                                                  if param1 != param2: 
69                                                          self.data.d2ri[param2, param1, i] = self.data.d2ri[param1, param2, i] 
70