Author: bugman
Date: Thu Sep 12 20:58:58 2013
New Revision: 20991
URL: http://svn.gna.org/viewcvs/relax?rev=20991&view=rev
Log:
Created the Relax_disp.test_hansen_catia_input system test.
This is to check the output of the relax_disp.catia_input user function.
Modified:
branches/relax_disp/test_suite/system_tests/relax_disp.py
Modified: branches/relax_disp/test_suite/system_tests/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/relax_disp.py?rev=20991&r1=20990&r2=20991&view=diff
==============================================================================
--- branches/relax_disp/test_suite/system_tests/relax_disp.py (original)
+++ branches/relax_disp/test_suite/system_tests/relax_disp.py Thu Sep 12
20:58:58 2013
@@ -21,7 +21,7 @@
###############################################################################
# Python module imports.
-from os import sep
+from os import F_OK, access, sep
from shutil import rmtree
from tempfile import mkdtemp
@@ -282,6 +282,114 @@
self.assert_('test' not in cdp.clustering)
self.assertEqual(cdp.clustering['free spins'], [':2@N'])
self.assertEqual(cdp.clustering['cluster'], [':1@N', ':3@N'])
+
+
+ def test_hansen_catia_input(self):
+ """Conversion of Dr. Flemming Hansen's CPMG R2eff values into input
files for CATIA.
+
+ This uses the data from Dr. Flemming Hansen's paper at
http://dx.doi.org/10.1021/jp074793o. This is CPMG data with a fixed
relaxation time period.
+ """
+
+ # Load the state, preserving the temp directory.
+ tmpdir = ds.tmpdir
+ state = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'+sep+'r2eff_values'
+ self.interpreter.state.load(state, force=True)
+ ds.tmpdir = tmpdir
+
+ # The spin isotopes.
+ self.interpreter.spin.isotope("15N")
+
+ # Generate the input files.
+ self.interpreter.relax_disp.catia_input(dir=ds.tmpdir, force=True)
+
+ # Check the r2eff set files.
+ print("\nChecking the R2eff input set files.")
+ files = ['data_set_500.inp', 'data_set_500.inp']
+ for file in files:
+ self.assert_(access(tmpdir+sep+file, F_OK))
+ data_set_500 = [
+ "ID=500\n",
+ "Sfrq = 500\n",
+ "Temperature = 0.0\n",
+ "Nucleus = N15\n",
+ "Couplednucleus = H1\n",
+ "Time_equil = 0.0\n",
+ "Pwx_cp = 0.0\n",
+ "Taub = 0.0\n",
+ "Time_T2 = 0.03\n",
+ "Xcar = 0.0\n",
+ "Seqfil = CW_CPMG\n",
+ "Minerror = (2.%;0.5/s)\n",
+ "Basis = (Iph_7)\n",
+ "Format = (0;1;2)\n",
+ "DataDirectory = /tmp/tmpNjOGNG/input_r2eff\n",
+ "Data = (\n",
+ " [70N;spin_70_N_500.cpmg];\n",
+ " [71N;spin_71_N_500.cpmg];\n",
+ ")\n",
+ ]
+ file = open(tmpdir+sep+files[0])
+ lines = file.readlines()
+ file.close()
+ for i in range(len(data_set_500)):
+ # Skip the data directory, as this is a random file name.
+ if i == 14:
+ continue
+
+ self.assertEqual(data_set_500[i], lines[i])
+
+ # Check the r2eff files.
+ print("\nChecking the R2eff input files.")
+ files = ['spin_70_N_500.cpmg', 'spin_70_N_800.cpmg',
'spin_71_N_500.cpmg', 'spin_71_N_800.cpmg']
+ for file in files:
+ self.assert_(access(tmpdir+sep+'input_r2eff'+sep+file, F_OK))
+ spin_70_N_500 = [
+ "# nu_cpmg(Hz) R2(1/s)
Esd(R2)\n",
+ " 66.666600000000003 16.045540885533605
0.646182586603895\n",
+ " 133.333300000000008 14.877924861181727
0.506206534738327\n",
+ " 200.000000000000000 14.357820247260586
0.623258826244929\n",
+ " 266.666600000000017 12.664494620416516
0.601723131243350\n",
+ " 333.333300000000008 12.363204802467891
0.598039562082036\n",
+ " 400.000000000000000 11.092532381134513
0.582981323247310\n",
+ " 466.666600000000017 10.566090057649893
0.576963907270428\n",
+ " 533.333300000000008 9.805806894657803
0.468279337463354\n",
+ " 600.000000000000000 9.564300692201730
0.565861181427156\n",
+ " 666.666600000000017 9.015633750407980
0.559969731566749\n",
+ " 733.333300000000008 8.607764958055581
0.555675260323333\n",
+ " 800.000000000000000 8.279997179221338
0.552276093478159\n",
+ " 866.666600000000017 8.474535940963516
0.554288038563643\n",
+ " 933.333300000000008 8.158972897365194
0.457722426033180\n",
+ "1000.000000000000000 7.988630509501972
0.549292861468630\n"
+ ]
+ file = open(tmpdir+sep+'input_r2eff'+sep+files[0])
+ lines = file.readlines()
+ file.close()
+ for i in range(len(spin_70_N_500)):
+ self.assertEqual(spin_70_N_500[i], lines[i])
+
+ # Check the main file.
+ print("\nChecking the main CATIA execution file.")
+ main_file = [
+ "ReadDataset(data_set_500.inp)\n",
+ "ReadDataset(data_set_800.inp)\n",
+ "ReadParam_Global(ParamGlobal.inp)\n",
+ "ReadParam_Local(ParamSet1.inp)\n",
+ "\n",
+ "Minimize(print=y;tol=1e-25;maxiter=10000000)\n",
+ "\n",
+ "PrintParam(output/GlobalParam.fit;global)\n",
+ "PrintParam(output/DeltaOmega.fit;DeltaO)\n",
+ "PrintData(output/)\n",
+ "\n",
+ "ChiSq(all;all)\n",
+ "exit(0)\n"
+ ]
+ file = open("%s%sFit.catia" % (ds.tmpdir, sep))
+ lines = file.readlines()
+ file.close()
+ for i in range(len(main_file)):
+ self.assertEqual(main_file[i], lines[i])
+
def test_hansen_cpmg_data_auto_analysis(self):
r20991 - /branches/relax_disp/test_suite/system_tests/relax_disp.py