[Cctbx-cvs] SF.net SVN: cctbx: [6169] trunk/mmtbx/mmtbx/refinement

[<af...@us...>]

Revision: 6169
          http://cctbx.svn.sourceforge.net/cctbx/?rev=6169&view=rev
Author:   afonine
Date:     2007-08-16 18:01:36 -0700 (Thu, 16 Aug 2007)

Log Message:
-----------
broken XN test fixed (forgotten flag added)

Modified Paths:
--------------
    trunk/mmtbx/mmtbx/refinement/adp_refinement.py
    trunk/mmtbx/mmtbx/refinement/minimization.py

Modified: trunk/mmtbx/mmtbx/refinement/adp_refinement.py
===================================================================
--- trunk/mmtbx/mmtbx/refinement/adp_refinement.py	2007-08-16 14:48:52 UTC (rev 6168)
+++ trunk/mmtbx/mmtbx/refinement/adp_refinement.py	2007-08-17 01:01:36 UTC (rev 6169)
@@ -116,6 +116,7 @@
             neutron_scattering_dict   = None,
             xray_scattering_dict      = None,
             wxnu_scale                = None,
+            use_xn_grads_filtering    = None,
             h_params                  = None):
     global time_adp_refinement_py
     timer = user_plus_sys_time()
@@ -202,6 +203,7 @@
                           neutron_scattering_dict  = neutron_scattering_dict,
                           xray_scattering_dict     = xray_scattering_dict,
                           wxnu_scale               = wxnu_scale,
+                          use_xn_grads_filtering   = use_xn_grads_filtering,
                           h_params                 = h_params)
        self.minimized.collector.show(text = "LBFGS minimization", out  = log)
        assert fmodel.xray_structure is model.xray_structure

Modified: trunk/mmtbx/mmtbx/refinement/minimization.py
===================================================================
--- trunk/mmtbx/mmtbx/refinement/minimization.py	2007-08-16 14:48:52 UTC (rev 6168)
+++ trunk/mmtbx/mmtbx/refinement/minimization.py	2007-08-17 01:01:36 UTC (rev 6169)
@@ -40,6 +40,7 @@
                      occupancy_max            = None,
                      occupancy_min            = None,
                      h_params                 = None,
+                     use_xn_grads_filtering   = None,
                      u_min                    = adptbx.b_as_u(-100.0),
                      u_max                    = adptbx.b_as_u(1000.0)):
     global time_site_individual
@@ -248,33 +249,35 @@
           if(self.refine_xyz):
              tt = flex.vec3_double(self.g)
              rr = flex.vec3_double(sf)
-             #for i, j, fd in zip(tt, rr, self.hd_selection):
-             #  angle = flex.double(i).angle(flex.double(j), deg = True)
-             #  if(angle >= 90.0):
-             #     if(fd): tt[ii] = [0,0,0]
-             #     else:   rr[ii] = [0,0,0]
-             #     #tt[ii] = [0,0,0]
-             #     #rr[ii] = [0,0,0]
-             #     #if(fd): tt[ii] = [tt[ii][0]/angle,tt[ii][1]/angle,tt[ii][2]/angle]
-             #     #else:   rr[ii] = [rr[ii][0]/angle,rr[ii][1]/angle,rr[ii][2]/angle]
-             #     #tt[ii] = [tt[ii][0]/angle,tt[ii][1]/angle,tt[ii][2]/angle]
-             #     #rr[ii] = [rr[ii][0]/angle,rr[ii][1]/angle,rr[ii][2]/angle]
-             #  ii += 1
+             if(self.use_xn_grads_filtering):
+               for i, j, fd in zip(tt, rr, self.hd_selection):
+                 angle = flex.double(i).angle(flex.double(j), deg = True)
+                 if(angle >= 90.0):
+                    if(fd): tt[ii] = [0,0,0]
+                    else:   rr[ii] = [0,0,0]
+                    #tt[ii] = [0,0,0]
+                    #rr[ii] = [0,0,0]
+                    #if(fd): tt[ii] = [tt[ii][0]/angle,tt[ii][1]/angle,tt[ii][2]/angle]
+                    #else:   rr[ii] = [rr[ii][0]/angle,rr[ii][1]/angle,rr[ii][2]/angle]
+                    #tt[ii] = [tt[ii][0]/angle,tt[ii][1]/angle,tt[ii][2]/angle]
+                    #rr[ii] = [rr[ii][0]/angle,rr[ii][1]/angle,rr[ii][2]/angle]
+                 ii += 1
              self.g = tt.as_double() + rr.as_double() * self.wn
           if(self.refine_adp):
              tt = self.g
              rr = sf
-             #for i, j, fd in zip(tt, rr, self.hd_selection):
-             #  if(i*j < 0):
-             #     if(fd): tt[ii] = 0.
-             #     else:   rr[ii] = 0.
-             #     #tt[ii] = 0.0
-             #     #rr[ii] = 0.0
-             #     #if(fd): tt[ii] = tt[ii]/3.
-             #     #else:   rr[ii] = rr[ii]/3.
-             #     #tt[ii] = tt[ii]/3.
-             #     #rr[ii] = rr[ii]/3.
-             #  ii += 1
+             if(self.use_xn_grads_filtering):
+               for i, j, fd in zip(tt, rr, self.hd_selection):
+                 if(i*j < 0):
+                    if(fd): tt[ii] = 0.
+                    else:   rr[ii] = 0.
+                    #tt[ii] = 0.0
+                    #rr[ii] = 0.0
+                    #if(fd): tt[ii] = tt[ii]/3.
+                    #else:   rr[ii] = rr[ii]/3.
+                    #tt[ii] = tt[ii]/3.
+                    #rr[ii] = rr[ii]/3.
+                 ii += 1
              self.g = tt + rr * self.wn
 
     if(self.refine_xyz and self.restraints_manager is not None and self.wr > 0.0):


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