OK, thanks Nick - it is actually good to know as we have been working on that one too... So we will synchronise it with you before committing,
Best wishes,
Oleg.
________________________________
From: [email protected] on behalf of Nicholas Sauter
Sent: 05 September 2018 16:57:28
To: cctbx mailing list
Cc: [email protected]
Subject: Re: [cctbxbb] [git/cctbx] master: re-defining the shift/est convergence limit in terms of crystallographic rather than independent parameters to make it easier to relate to the convergence reported in the CIF; also caching the shifts for further analys...
OK, I've had a chance to run the tests and everything seems to check out. For XFEL we use the "levenberg_marquardt_iterations_encapsulated_eqns" that seems to be not affected by your code commit.
Nick
Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713
On Wed, Sep 5, 2018 at 8:42 AM, [email protected]mailto:[email protected] mailto:[email protected]> wrote:
Sorry Nick,
please let me know - I can pull it back or tweak as needed...
Cheers,
Oleg.
________________________________
From: [email protected]mailto:[email protected] mailto:[email protected]> on behalf of Nicholas Sauter mailto:[email protected]>
Sent: 05 September 2018 16:37:53
To: cctbx mailing list
Cc: [email protected]mailto:[email protected]
Subject: Re: [cctbxbb] [git/cctbx] master: re-defining the shift/est convergence limit in terms of crystallographic rather than independent parameters to make it easier to relate to the convergence reported in the CIF; also caching the shifts for further analys...
I'm worried about making changes like this to a fundamental toolbox component like normal equations solving. We use this for processing xfel data, and would like the opportunity to test any changes through a pull request, prior to having them committed to the main branch.
Nick Sauter
Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713
On Wed, Sep 5, 2018 at 5:29 AM, CCTBX commit mailto:[email protected]> wrote:
Repository : ssh://g18-sc-serv-04.diamond.ac.uk/cctbxhttp://g18-sc-serv-04.diamond.ac.uk/cctbx
On branch : master
________________________________
commit 9339fd5f7d240f0d6f85dd57ce42e796d19608f1
Author: pcxod mailto:[email protected]>
Date: Wed Sep 5 13:29:29 2018 +0100
re-defining the shift/est convergence limit in terms of crystallographic rather than independent parameters to make it easier to relate to the convergence reported in the CIF; also caching the shifts for further analysis and reporting;
________________________________
9339fd5f7d240f0d6f85dd57ce42e796d19608f1
scitbx/lstbx/normal_eqns_solving.py | 17 +++++++++++------
1 file changed, 11 insertions(+), 6 deletions(-)
diff --git a/scitbx/lstbx/normal_eqns_solving.py b/scitbx/lstbx/normal_eqns_solving.py
index 660304eab..45f070622 100644
--- a/scitbx/lstbx/normal_eqns_solving.py
+++ b/scitbx/lstbx/normal_eqns_solving.py
@@ -140,15 +140,20 @@ class iterations(object):
a = self.non_linear_ls.normal_matrix_packed_u()
a.matrix_packed_u_diagonal_add_in_place(value*a.matrix_packed_u_diagonal())
- def do_scale_shifts(self, max_shift_over_esd):
+ def do_scale_shifts(self, limit_shift_over_su):
x = self.non_linear_ls.step()
esd = self.non_linear_ls.covariance_matrix().matrix_packed_u_diagonal()
- x_over_esd = flex.abs(x/flex.sqrt(esd))
- max_val = flex.max(x_over_esd)
- if max_val < self.convergence_as_shift_over_esd:
+ ls_shifts_over_su = flex.abs(x/flex.sqrt(esd))
+ #max shift for the LS
+ self.max_ls_shift_over_su = flex.max(ls_shifts_over_su)
+ jac_tr = self.non_linear_ls.actual.\
+ reparametrisation.jacobian_transpose_matching_grad_fc()
+ self.shifts_over_su = jac_tr.transpose() * ls_shifts_over_su
+ self.max_shift_over_su = flex.max(self.shifts_over_su)
+ if self.max_shift_over_su < self.convergence_as_shift_over_esd:
return True
- if max_val > max_shift_over_esd:
- shift_scale = max_shift_over_esd/max_val
+ if self.max_ls_shift_over_su > limit_shift_over_su:
+ shift_scale = limit_shift_over_su/self.max_ls_shift_over_su
x *= shift_scale
return False
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