Author: bugman
Date: Fri Sep 13 13:54:51 2013
New Revision: 20999
URL: http://svn.gna.org/viewcvs/relax?rev=20999&view=rev
Log:
Added the CATIA input files generated by relax for Flemming Hansen's
truncated CPMG data set.
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/Fit.catia
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamGlobal.inp
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamSet1.inp
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/catia.log
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_500.inp
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_800.inp
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_500.cpmg
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_800.cpmg
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_500.cpmg
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_800.cpmg
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/output/
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/Fit.catia
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/Fit.catia?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/Fit.catia
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/Fit.catia
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,13 @@
+ReadDataset(data_set_500.inp)
+ReadDataset(data_set_800.inp)
+ReadParam_Global(ParamGlobal.inp)
+ReadParam_Local(ParamSet1.inp)
+
+Minimize(print=y;tol=1e-25;maxiter=10000000)
+
+PrintParam(output/GlobalParam.fit;global)
+PrintParam(output/DeltaOmega.fit;DeltaO)
+PrintData(output/)
+
+ChiSq(all;all)
+exit(0)
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamGlobal.inp
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamGlobal.inp?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamGlobal.inp
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamGlobal.inp
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,2 @@
+kex = 1500.0
+pb = 0.05
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamSet1.inp
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamSet1.inp?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamSet1.inp
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/ParamSet1.inp
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,2 @@
+format = (Delta0;R0iph_500;R0iph_800)
+* = (0.5;5.0;5.0)
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/catia.log
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/catia.log?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/catia.log
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/catia.log
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,98 @@
+
+
+
+ relax repository checkout r20990
+
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp
+
+ Molecular dynamics by NMR data analysis
+
+ Copyright (C) 2001-2006 Edward d'Auvergne
+ Copyright (C) 2006-2013 the relax development team
+
+This is free software which you are welcome to modify and redistribute under
the conditions of the
+GNU General Public License (GPL). This program, including all modules, is
licensed under the GPL
+and comes with absolutely no warranty. For details type 'GPL' within the
relax prompt.
+
+Assistance in using the relax prompt and scripting interface can be accessed
by typing 'help' within
+the prompt.
+
+Processor fabric: Uni-processor.
+
+script = 'catia.py'
+----------------------------------------------------------------------------------------------------
+"""Script for generating input files for CATIA and running CATIA.
+
+To run:
+
+$ ../../../../../relax --tee catia.log catia.py
+"""
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from status import Status; status = Status()
+
+
+# Load the saved state.
+data_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'dispersion'+sep+'Hansen'
+state.load(data_path+sep+'r2eff_values')
+
+# Set up the spin isotope information.
+spin.isotope('15N')
+
+# Generate the CATIA input files.
+relax_disp.catia_input(dir='.', force=True)
+
+# Execute CATIA.
+relax_disp.catia_execute()
+----------------------------------------------------------------------------------------------------
+
+relax>
state.load(state='/data/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/r2eff_values',
dir=None, force=False)
+Opening the file
'/data/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/r2eff_values.bz2'
for reading.
+
+relax> spin.isotope(isotope='15N', spin_id=None, force=False)
+
+relax> relax_disp.catia_input(dir='.', force=True)
+Opening the file './data_set_500.inp' for writing.
+Opening the file './input_r2eff/spin_70_N_500.cpmg' for writing.
+Opening the file './input_r2eff/spin_71_N_500.cpmg' for writing.
+Opening the file './data_set_800.inp' for writing.
+Opening the file './input_r2eff/spin_70_N_800.cpmg' for writing.
+Opening the file './input_r2eff/spin_71_N_800.cpmg' for writing.
+Opening the file './ParamGlobal.inp' for writing.
+Opening the file './ParamSet1.inp' for writing.
+Opening the file './Fit.catia' for writing.
+
+relax> relax_disp.catia_execute(dir=None, binary='catia')
+ *
+ * --- CATIA ---
+ * (Cpmg, Antitrosy, and Trosy Intelligent Analysis)
+ * Version 0.51p
+ *
+ * Copyright 2007-2008 by D. Flemming Hansen (DFH)
+ * All rights reserved.
+ *
+ * This software and its related software and documentation is provided
+ * 'as is' without express or implied warrenty. The author (DFH) makes no
+ * warrenties as to any matter whatsoever with respect to the program
+ * and the related software and documentation. In particular, any and all
+ * warranties of merchantability and fitness for any particular purpose
+ * are expressly excluded.
+ *
+ * flemming@xxxxxxxxxxxxxxxxxxxxx
+ *
+ *
+ * If you use this program to conduct academic research you should cite
+ * the program as:
+ *
+ * CATIA (Cpmg, Anti-trosy, and Trosy Intelligent Analysis) version 0.51p
+ * (2008); D. Flemming Hansen
+ *
+CATIA>CATIA>CATIA>CATIA>CATIA>CATIA> The parameters:R1iph_500 is required by
the basisset Iph_7
+ but is not provided for atom 70N
+ please provide in the LocalParameter set
+ Function FreePrecess_Iph_7()
+
+ CATIA_ABORT has been called with error status: 1
+
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_500.inp
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_500.inp?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_500.inp
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_500.inp
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,19 @@
+ID=500
+Sfrq = 500
+Temperature = 0.0
+Nucleus = N15
+Couplednucleus = H1
+Time_equil = 0.0
+Pwx_cp = 0.0
+Taub = 0.0
+Time_T2 = 0.03
+Xcar = 0.0
+Seqfil = CW_CPMG
+Minerror = (2.%;0.5/s)
+Basis = (Iph_7)
+Format = (0;1;2)
+DataDirectory = ./input_r2eff/
+Data = (
+ [70N;spin_70_N_500.cpmg];
+ [71N;spin_71_N_500.cpmg];
+)
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_800.inp
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_800.inp?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_800.inp
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/data_set_800.inp
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,19 @@
+ID=800
+Sfrq = 800
+Temperature = 0.0
+Nucleus = N15
+Couplednucleus = H1
+Time_equil = 0.0
+Pwx_cp = 0.0
+Taub = 0.0
+Time_T2 = 0.03
+Xcar = 0.0
+Seqfil = CW_CPMG
+Minerror = (2.%;0.5/s)
+Basis = (Iph_7)
+Format = (0;1;2)
+DataDirectory = ./input_r2eff/
+Data = (
+ [70N;spin_70_N_800.cpmg];
+ [71N;spin_71_N_800.cpmg];
+)
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_500.cpmg
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_500.cpmg?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_500.cpmg
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_500.cpmg
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,16 @@
+# nu_cpmg(Hz) R2(1/s) Esd(R2)
+ 66.666600000000003 16.045540885533605 0.646182586603895
+ 133.333300000000008 14.877924861181727 0.506206534738327
+ 200.000000000000000 14.357820247260586 0.623258826244929
+ 266.666600000000017 12.664494620416516 0.601723131243350
+ 333.333300000000008 12.363204802467891 0.598039562082036
+ 400.000000000000000 11.092532381134513 0.582981323247310
+ 466.666600000000017 10.566090057649893 0.576963907270428
+ 533.333300000000008 9.805806894657803 0.468279337463354
+ 600.000000000000000 9.564300692201730 0.565861181427156
+ 666.666600000000017 9.015633750407980 0.559969731566749
+ 733.333300000000008 8.607764958055581 0.555675260323333
+ 800.000000000000000 8.279997179221338 0.552276093478159
+ 866.666600000000017 8.474535940963516 0.554288038563643
+ 933.333300000000008 8.158972897365194 0.457722426033180
+1000.000000000000000 7.988630509501972 0.549292861468630
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_800.cpmg
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_800.cpmg?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_800.cpmg
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_70_N_800.cpmg
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,16 @@
+# nu_cpmg(Hz) R2(1/s) Esd(R2)
+ 66.666600000000003 22.224914187017955 0.278879133984032
+ 133.333300000000008 21.230874263054286 0.212640524601906
+ 200.000000000000000 20.603704070506069 0.268455371759799
+ 266.666600000000017 20.327797401799192 0.266742193240964
+ 333.333300000000008 18.855377144166454 0.257889209709764
+ 400.000000000000000 18.537530893451883 0.256040939675177
+ 466.666600000000017 17.508069423326553 0.250203656956424
+ 533.333300000000008 16.035603819868157 0.193522950529860
+ 600.000000000000000 15.168191575096751 0.237753891087126
+ 666.666600000000017 14.431802236880866 0.234061703303284
+ 733.333300000000008 14.034137303142154 0.232111327489284
+ 800.000000000000000 12.920148216311929 0.226806520505883
+ 866.666600000000017 12.653673349582139 0.225571664982831
+ 933.333300000000008 12.610863989976654 0.183051658421605
+1000.000000000000000 11.969303192678483 0.222459361025708
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_500.cpmg
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_500.cpmg?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_500.cpmg
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_500.cpmg
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,16 @@
+# nu_cpmg(Hz) R2(1/s) Esd(R2)
+ 66.666600000000003 7.044342457026060 0.353377264211502
+ 133.333300000000008 6.781032716546586 0.294218251707417
+ 200.000000000000000 6.467622614080504 0.349728013619598
+ 266.666600000000017 6.333339827307936 0.348890956500757
+ 333.333300000000008 6.323238193341627 0.348828179033842
+ 400.000000000000000 6.005245039869958 0.346865612794037
+ 466.666600000000017 5.767051993948105 0.345412753181991
+ 533.333300000000008 5.476967601293420 0.289430537091687
+ 600.000000000000000 5.469948766899343 0.343621033966560
+ 666.666600000000017 5.295113207914031 0.342577201745335
+ 733.333300000000008 5.435647509638665 0.343415629568723
+ 800.000000000000000 5.410399932309044 0.343264632376150
+ 866.666600000000017 5.437553763491596 0.343427036818110
+ 933.333300000000008 5.176844226808310 0.288370071024094
+1000.000000000000000 5.227231917975078 0.342174017277569
Added:
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_800.cpmg
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_800.cpmg?rev=20999&view=auto
==============================================================================
---
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_800.cpmg
(added)
+++
branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results/input_r2eff/spin_71_N_800.cpmg
Fri Sep 13 13:54:51 2013
@@ -1,0 +1,1 @@
+# nu_cpmg(Hz) R2(1/s) Esd(R2)
r20999 - in /branches/relax_disp/test_suite/shared_data/dispersion/Hansen/catia_results: ./ input_r2eff/ output/