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[Cctbx-cvs] mmtbx/mmtbx/bulk_solvent bulk_solvent_and_scaling.py, 1.8.2.2, 1.8.2.3 tst_bulk_solvent_and_scaling_ls.py, 1.5.2.1, 1.5.2.2 tst_bulk_solvent_and_scaling_ml.py, 1.4.2.1, 1.4.2.2
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From: Ralf W. Grosse-K. <rw...@us...> - 2006-07-01 01:12:19
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Update of /cvsroot/cctbx/mmtbx/mmtbx/bulk_solvent In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv32526/mmtbx/bulk_solvent Modified Files: Tag: phenix_rc_2006_07 bulk_solvent_and_scaling.py tst_bulk_solvent_and_scaling_ls.py tst_bulk_solvent_and_scaling_ml.py Log Message: fix cvs problems: missing updated from trunk Index: tst_bulk_solvent_and_scaling_ls.py =================================================================== RCS file: /cvsroot/cctbx/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ls.py,v retrieving revision 1.5.2.1 retrieving revision 1.5.2.2 diff -C2 -d -r1.5.2.1 -r1.5.2.2 *** tst_bulk_solvent_and_scaling_ls.py 27 Jun 2006 01:31:46 -0000 1.5.2.1 --- tst_bulk_solvent_and_scaling_ls.py 1 Jul 2006 01:12:08 -0000 1.5.2.2 *************** *** 119,123 **** fmodel.update_solvent_and_scale(params = params) assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-3, tb = 0.5, tu = 1.e-1) print "OK: LS min.&grid s.: ",format_cpu_times() --- 119,123 ---- fmodel.update_solvent_and_scale(params = params) assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-3, tb = 0.05, tu = 1.e-3) print "OK: LS min.&grid s.: ",format_cpu_times() *************** *** 159,163 **** fmodel.update_solvent_and_scale(params = params) assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 0.05, tb = 11.0, tu = 1.e-1) print "OK: LS minimization: ",format_cpu_times() --- 159,163 ---- fmodel.update_solvent_and_scale(params = params) assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 0.00001, tb = 0.01, tu = 1.e-3) print "OK: LS minimization: ",format_cpu_times() *************** *** 602,608 **** params.k_sol_b_sol_grid_search = True params.minimization_k_sol_b_sol = True ! params.minimization_b_cart = True params.target = "ls_wunit_k1" ! params.symmetry_constraints_on_b_cart = True params.k_sol_max = 0.8 params.k_sol_min = 0.1 --- 602,608 ---- params.k_sol_b_sol_grid_search = True params.minimization_k_sol_b_sol = True ! params.minimization_b_cart = True params.target = "ls_wunit_k1" ! params.symmetry_constraints_on_b_cart = True params.k_sol_max = 0.8 params.k_sol_min = 0.1 *************** *** 610,614 **** params.b_sol_min = 10.0 params.k_sol_step = 0.02 ! params.b_sol_step = 1.0 params.number_of_macro_cycles = 10 params.number_of_minimization_macro_cycles = 10 --- 610,614 ---- params.b_sol_min = 10.0 params.k_sol_step = 0.02 ! params.b_sol_step = 5.0 params.number_of_macro_cycles = 10 params.number_of_minimization_macro_cycles = 10 *************** *** 616,628 **** params.fix_k_sol = None params.fix_b_sol = None ! params.fix_b_cart = None params.start_minimization_from_k_sol = 0.35 params.start_minimization_from_b_sol = 46.0 ! params.start_minimization_from_b_cart = [0,0,0,0,0,0] ! params.apply_back_trace_of_b_cart = False fmodel_copy.update_solvent_and_scale(params = params) assert_result(fmodel_copy, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-2, tb = 5., tu = 0.5) print "OK: closest to real: ",format_cpu_times() --- 616,628 ---- params.fix_k_sol = None params.fix_b_sol = None ! params.fix_b_cart = None params.start_minimization_from_k_sol = 0.35 params.start_minimization_from_b_sol = 46.0 ! params.start_minimization_from_b_cart = [0,0,0,0,0,0] ! params.apply_back_trace_of_b_cart = False fmodel_copy.update_solvent_and_scale(params = params) assert_result(fmodel_copy, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-2, tb = 6., tu = 0.5) print "OK: closest to real: ",format_cpu_times() Index: bulk_solvent_and_scaling.py =================================================================== RCS file: /cvsroot/cctbx/mmtbx/mmtbx/bulk_solvent/bulk_solvent_and_scaling.py,v retrieving revision 1.8.2.2 retrieving revision 1.8.2.3 diff -C2 -d -r1.8.2.2 -r1.8.2.3 *** bulk_solvent_and_scaling.py 27 Jun 2006 01:31:46 -0000 1.8.2.2 --- bulk_solvent_and_scaling.py 1 Jul 2006 01:12:08 -0000 1.8.2.3 *************** *** 38,42 **** k_sol_min = 0.0 .type = float ! b_sol_max = 80.0 .type = float b_sol_min = 10.0 --- 38,42 ---- k_sol_min = 0.0 .type = float ! b_sol_max = 100.0 .type = float b_sol_min = 10.0 *************** *** 509,520 **** ksol = fmodel.k_sol bsol = fmodel.b_sol ! kb_min_done = False ! b_cart_min_done = False for mc in macro_cycles: - outf = params.verbose > 0 and mc==macro_cycles[len(macro_cycles)-1] do_grid_search = (ksol<params.k_sol_min or ksol>params.k_sol_max or bsol<params.b_sol_min or ksol>params.b_sol_max) ! #print "do_grid_search = ",do_grid_search ! if(params.k_sol_b_sol_grid_search and do_grid_search): for ksol_ in k_sols: for bsol_ in b_sols: --- 509,519 ---- ksol = fmodel.k_sol bsol = fmodel.b_sol ! grid_search_done = False for mc in macro_cycles: do_grid_search = (ksol<params.k_sol_min or ksol>params.k_sol_max or bsol<params.b_sol_min or ksol>params.b_sol_max) ! if(params.k_sol_b_sol_grid_search and do_grid_search and ! not grid_search_done): ! grid_search_done = True for ksol_ in k_sols: for bsol_ in b_sols: *************** *** 526,547 **** bsol = bsol_ fmodel.update(k_sol = ksol, b_sol = bsol) ! if(outf): h=m+str(mc)+": k & b: grid search; T= "+fmodel.target_name fmodel.show_k_sol_b_sol_b_cart_target(header = h, out = log) ! if((params.k_sol_b_sol_grid_search,params.minimization_k_sol_b_sol)\ ! == (False,True) and do_grid_search): ! fmodel.update(k_sol = params.start_minimization_from_k_sol, ! b_sol = params.start_minimization_from_b_sol, ! b_cart = params.start_minimization_from_b_cart) ! ksol, bsol = k_sol_b_sol_minimizer(fmodel = fmodel) ! kb_min_done = True ! fmodel.update(k_sol = ksol, b_sol = bsol) ! if(outf): h=m+str(mc)+": k & b: minimization; T= "+fmodel.target_name fmodel.show_k_sol_b_sol_b_cart_target(header = h, out = log) ! if(params.minimization_b_cart and do_grid_search): self._b_cart_minimizer_helper(params, fmodel) ! b_cart_min_done = True ! if(outf): h=m+str(mc)+": anisotropic scale; T= "+fmodel.target_name fmodel.show_k_sol_b_sol_b_cart_target(header = h, out = log) --- 525,539 ---- bsol = bsol_ fmodel.update(k_sol = ksol, b_sol = bsol) ! if(params.verbose > 0): h=m+str(mc)+": k & b: grid search; T= "+fmodel.target_name fmodel.show_k_sol_b_sol_b_cart_target(header = h, out = log) ! if(params.minimization_k_sol_b_sol): ! self._k_sol_b_sol_minimization_helper(params, fmodel) ! if(params.verbose > 0): h=m+str(mc)+": k & b: minimization; T= "+fmodel.target_name fmodel.show_k_sol_b_sol_b_cart_target(header = h, out = log) ! if(params.minimization_b_cart): self._b_cart_minimizer_helper(params, fmodel) ! if(params.verbose > 0): h=m+str(mc)+": anisotropic scale; T= "+fmodel.target_name fmodel.show_k_sol_b_sol_b_cart_target(header = h, out = log) *************** *** 556,591 **** # h=m+str(mc)+": (ordered solvent) T= "+self.target_name # self.show_k_sol_b_sol_b_cart_target(header = h, out = log) - if([params.minimization_k_sol_b_sol, - params.minimization_b_cart].count(True) > 0 and - [kb_min_done,b_cart_min_done].count(False) > 0): - for mc in minimization_macro_cycles: - outf = params.verbose > 0 and \ - mc==minimization_macro_cycles[len(minimization_macro_cycles)-1] - if(params.minimization_k_sol_b_sol and not kb_min_done): - self._k_sol_b_sol_minimization_helper(params, fmodel) - if(outf): - h=m+str(mc)+": k_sol & b_sol min.; T= "+fmodel.target_name - fmodel.show_k_sol_b_sol_b_cart_target(header=h, out = log) - if(params.minimization_b_cart and not b_cart_min_done): - self._b_cart_minimizer_helper(params, fmodel) - if(outf): - h=m+str(mc)+": anisotropic scale; T= "+fmodel.target_name - fmodel.show_k_sol_b_sol_b_cart_target(header=h, out = log) ### start ml optimization if(abs(fmodel.k_sol) < 0.01 or abs(fmodel.b_sol) < 1.0): fmodel.update(k_sol = 0, b_sol = 0) ! if(params_target == "ml"): #XXX temporary OFF; use ls for the moment ! #if(params_target == "ls_wunit_k1"): params.target = params_target fmodel.update(target_name = params_target) if(params.minimization_k_sol_b_sol): for mc in minimization_macro_cycles: - outf = params.verbose > 0 and mc == \ - minimization_macro_cycles[len(minimization_macro_cycles)-1] self._k_sol_b_sol_minimization_helper(params, fmodel) ! if(outf): h=m+str(mc)+": k_sol & b_sol min.; T= "+fmodel.target_name fmodel.show_k_sol_b_sol_b_cart_target(header=h, out = log) - fmodel.update(target_name = fmodel_target) if(fmodel.alpha_beta_params is not None): fmodel.alpha_beta_params.interpolation = save_interpolation_flag --- 548,568 ---- # h=m+str(mc)+": (ordered solvent) T= "+self.target_name # self.show_k_sol_b_sol_b_cart_target(header = h, out = log) ### start ml optimization if(abs(fmodel.k_sol) < 0.01 or abs(fmodel.b_sol) < 1.0): fmodel.update(k_sol = 0, b_sol = 0) ! ! ksol = fmodel.k_sol ! bsol = fmodel.b_sol ! bcart= fmodel.b_cart ! r_work = fmodel.r_work() ! if(params_target == "ml"): params.target = params_target fmodel.update(target_name = params_target) if(params.minimization_k_sol_b_sol): for mc in minimization_macro_cycles: self._k_sol_b_sol_minimization_helper(params, fmodel) ! if(params.verbose > 0): h=m+str(mc)+": k_sol & b_sol min.; T= "+fmodel.target_name fmodel.show_k_sol_b_sol_b_cart_target(header=h, out = log) if(fmodel.alpha_beta_params is not None): fmodel.alpha_beta_params.interpolation = save_interpolation_flag *************** *** 612,616 **** fmodel.update(b_cart = b_cart) r_final = fmodel.r_work() ! if(r_final - r_start > 0.005): print "Warning: r went up after anisotropic scaling:" print " r_start = ", r_start --- 589,593 ---- fmodel.update(b_cart = b_cart) r_final = fmodel.r_work() ! if(r_final - r_start > 0.01): print "Warning: r went up after anisotropic scaling:" print " r_start = ", r_start *************** *** 622,627 **** def _k_sol_b_sol_minimization_helper(self, params, fmodel): ksol_orig, bsol_orig = fmodel.k_sol_b_sol() - ksol, bsol = k_sol_b_sol_minimizer(fmodel = fmodel) r_start = fmodel.r_work() if(ksol <= params.k_sol_min or ksol >= params.k_sol_max): k1 = abs(abs(ksol) - abs(params.k_sol_min)) --- 599,604 ---- def _k_sol_b_sol_minimization_helper(self, params, fmodel): ksol_orig, bsol_orig = fmodel.k_sol_b_sol() r_start = fmodel.r_work() + ksol, bsol = k_sol_b_sol_minimizer(fmodel = fmodel) if(ksol <= params.k_sol_min or ksol >= params.k_sol_max): k1 = abs(abs(ksol) - abs(params.k_sol_min)) Index: tst_bulk_solvent_and_scaling_ml.py =================================================================== RCS file: /cvsroot/cctbx/mmtbx/mmtbx/bulk_solvent/tst_bulk_solvent_and_scaling_ml.py,v retrieving revision 1.4.2.1 retrieving revision 1.4.2.2 diff -C2 -d -r1.4.2.1 -r1.4.2.2 *** tst_bulk_solvent_and_scaling_ml.py 27 Jun 2006 01:31:46 -0000 1.4.2.1 --- tst_bulk_solvent_and_scaling_ml.py 1 Jul 2006 01:12:08 -0000 1.4.2.2 *************** *** 119,123 **** assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-3, tb = 0.5, tu = 1.e-1) print "OK: ML min.&grid s.: ",format_cpu_times() --- 119,123 ---- assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-3, tb = 0.3, tu = 1.e-2) print "OK: ML min.&grid s.: ",format_cpu_times() *************** *** 159,163 **** assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-2, tb = 10, tu = 1.e-1) print "OK: ML minimization: ",format_cpu_times() --- 159,163 ---- assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-2, tb = 0.3, tu = 1.e-2) print "OK: ML minimization: ",format_cpu_times() *************** *** 241,245 **** assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-6, tb = 1.e-6, tu = 1.e-1) print "OK: ML fix_ksolbsol: ",format_cpu_times() --- 241,245 ---- assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-6, tb = 1.e-6, tu = 1.e-3) print "OK: ML fix_ksolbsol: ",format_cpu_times() *************** *** 453,457 **** assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-6, tb = 1.e-6, tu = 1.e-1) print "OK: exercise_7: ",format_cpu_times() --- 453,457 ---- assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-6, tb = 1.e-6, tu = 1.e-3) print "OK: exercise_7: ",format_cpu_times() *************** *** 495,499 **** assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-6, tb = 1.e-6, tu = 1.e-1) print "OK: exercise_8: ",format_cpu_times() --- 495,499 ---- assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-6, tb = 1.e-6, tu = 1.e-3) print "OK: exercise_8: ",format_cpu_times() *************** *** 536,540 **** assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-4, tb = 1.e-1, tu = 1.e-6) print "OK: exercise_9: ",format_cpu_times() --- 536,540 ---- assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-5, tb = 1.e-6, tu = 1.e-6) print "OK: exercise_9: ",format_cpu_times() *************** *** 577,581 **** assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-4, tb = 1.e-1, tu = 1.e-6) print "OK: exercise_10: ",format_cpu_times() --- 577,581 ---- assert_result(fmodel, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-5, tb = 1.e-2, tu = 1.e-6) print "OK: exercise_10: ",format_cpu_times() *************** *** 624,628 **** fmodel_copy.update_solvent_and_scale(params = params) assert_result(fmodel_copy, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-3, tb = 5.e-1, tu = 0.2) print "OK: closest to real: ",format_cpu_times() --- 624,628 ---- fmodel_copy.update_solvent_and_scale(params = params) assert_result(fmodel_copy, k_sol, b_sol, b_cart, f_obs, r_free_flags, ! tk = 1.e-4, tb = 0.001, tu = 0.001) print "OK: closest to real: ",format_cpu_times() |