Author: bugman
Date: Fri Sep 25 14:12:45 2015
New Revision: 27871
URL: http://svn.gna.org/viewcvs/relax?rev=27871&view=rev
Log:
Merged revisions 27846 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27846 | tlinnet | 2015-05-28 18:15:48 +0200 (Thu, 28 May 2015) | 3 lines
Added additional test to systemtest
Relax_disp.test_bug_23186_cluster_error_calc_dw() to prove that Bug #23619 is
invalid.
Bug #23619: (https://gna.org/bugs/index.php?23619): Stored chi2 sim values
from Monte-Carlo simulations does not equal normal chi2 values.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Sep 25 14:12:45 2015
@@ -1 +1 @@
-/trunk:1-27797,27800-27845
+/trunk:1-27797,27800-27846
Modified: branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py?rev=27871&r1=27870&r2=27871&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/relax_disp.py Fri
Sep 25 14:12:45 2015
@@ -23,7 +23,8 @@
# Python module imports.
from os import F_OK, access, getcwd, path, sep
-from numpy import array, asarray, exp, median, inf, linspace, log, save,
std, sum, zeros
+import copy
+from numpy import array, asarray, average, exp, median, inf, linspace, log,
save, std, sum, zeros
from minfx.generic import generic_minimise
from random import gauss
import re, math
@@ -1467,8 +1468,16 @@
# First get the resi 0 array of sim r2a.
resi_0_r2a = []
+ # Assign spins
+ res0 = cdp.mol[0].res[0].spin[0]
+ res1 = cdp.mol[0].res[1].spin[0]
+
+ print("Chi2 before call to minimise: %3.3f"%res0.chi2)
+ self.interpreter.minimise.execute(min_algor='simplex',
max_iter=100000, verbosity=0)
+ print("Chi2 after call to minimise: %3.3f"%res0.chi2)
+
# Loop over the dics in spin.
- for cdic in cdp.mol[0].res[0].spin[0].r2a_sim:
+ for cdic in res0.r2a_sim:
resi_0_r2a.append(cdic[dickey])
# Get stats with numpy
@@ -1478,7 +1487,7 @@
resi_86_r2a = []
# Loop over the dics in spin.
- for cdic in cdp.mol[0].res[1].spin[0].r2a_sim:
+ for cdic in res1.r2a_sim:
resi_86_r2a.append(cdic[dickey])
# Get stats with numpy
@@ -1487,8 +1496,8 @@
# Then get for dw.
# First get the array of sim dw.
- resi_0_dw = cdp.mol[0].res[0].spin[0].dw_sim
- resi_86_dw = cdp.mol[0].res[1].spin[0].dw_sim
+ resi_0_dw = res0.dw_sim
+ resi_86_dw = res1.dw_sim
# Get stats with numpy
resi_0_dw_std = std(asarray(resi_0_dw), ddof=1)
@@ -1497,8 +1506,8 @@
# Then get for spin independent parameter.
# First get the array of sim dw.
- resi_0_kAB = cdp.mol[0].res[0].spin[0].k_AB_sim
- resi_86_kAB = cdp.mol[0].res[1].spin[0].k_AB_sim
+ resi_0_kAB = res0.k_AB_sim
+ resi_86_kAB = res1.k_AB_sim
# Get stats with numpy
resi_0_kAB_std = std(asarray(resi_0_kAB), ddof=1)
@@ -1511,16 +1520,46 @@
self.interpreter.monte_carlo.error_analysis()
# Check values for k_AB.
- self.assertAlmostEqual(resi_0_kAB_std,
cdp.mol[0].res[0].spin[0].k_AB_err)
- self.assertAlmostEqual(resi_86_kAB_std,
cdp.mol[0].res[1].spin[0].k_AB_err)
+ self.assertAlmostEqual(resi_0_kAB_std, res0.k_AB_err)
+ self.assertAlmostEqual(resi_86_kAB_std, res1.k_AB_err)
# Check values for r2a.
- self.assertAlmostEqual(resi_0_r2a_std,
cdp.mol[0].res[0].spin[0].r2a_err[dickey])
- self.assertAlmostEqual(resi_86_r2a_std,
cdp.mol[0].res[1].spin[0].r2a_err[dickey])
+ self.assertAlmostEqual(resi_0_r2a_std, res0.r2a_err[dickey])
+ self.assertAlmostEqual(resi_86_r2a_std, res1.r2a_err[dickey])
# Check values for dw.
- self.assertAlmostEqual(resi_0_dw_std,
cdp.mol[0].res[0].spin[0].dw_err)
- self.assertAlmostEqual(resi_86_dw_std,
cdp.mol[0].res[1].spin[0].dw_err)
+ self.assertAlmostEqual(resi_0_dw_std, res0.dw_err)
+ self.assertAlmostEqual(resi_86_dw_std, res1.dw_err)
+
+ # The following is for Bug #23619:
(https://gna.org/bugs/index.php?23619): Stored chi2 sim values from
Monte-Carlo simulations does not equal normal chi2 values.
+ # This is to show that this bug is invalid. The "very" different
chi2 values stems from r2eff points being back-calculated values rather than
original measured values.
+
+ # Check calculates the same Monte-Carlo chi2 values
+ self.interpreter.monte_carlo.setup(number=3)
+ self.interpreter.monte_carlo.create_data(method='back_calc')
+ self.interpreter.monte_carlo.initial_values()
+
+ # Assign original data instead of back_calculated error.
+ res0.r2eff_sim[0] = copy.copy(res0.r2eff)
+ res0.r2eff_sim[1] = copy.copy(res0.r2eff)
+ res0.r2eff_sim[2] = copy.copy(res0.r2eff)
+ res1.r2eff_sim[0] = copy.copy(res1.r2eff)
+ res1.r2eff_sim[1] = copy.copy(res1.r2eff)
+ res1.r2eff_sim[2] = copy.copy(res1.r2eff)
+
+ self.interpreter.minimise.execute(min_algor='simplex',
max_iter=100000)
+ self.interpreter.monte_carlo.error_analysis()
+
+ # Get the simulation array and calculate the average
+ spin_chi2_mc = res0.chi2
+ spin_chi2_mc_sim = res0.chi2_sim
+ spin_chi2_mc_sim_ave = average(spin_chi2_mc_sim)
+
+ print("The chi2 from calculation is: %3.3f"%spin_chi2_mc)
+ print("The array with monte-carlo chi2 values is:
%s"%spin_chi2_mc_sim)
+ print("The average of this array is: %3.3f"%spin_chi2_mc_sim_ave)
+
+ self.assertAlmostEqual(spin_chi2_mc, spin_chi2_mc_sim_ave, 7)
def test_bug_9999_slow_r1rho_r2eff_error_with_mc(self):
r27871 - in /branches/frame_order_cleanup: ./ test_suite/system_tests/relax_disp.py