Thanks Troels, this also works!
Stefano
On Mar 18, 2014, at 5:22 PM, Troels Emtekær Linnet wrote:
> Or open the relax prompt
> Ctrl+p
>
> And write:
> script("script.py")
>
> ------------ OUT COME ---------
>
> script = 'script.py'
> ----------------------------------------------------------------------------------------------------
> # Python module imports.
> from numpy import float64, zeros
>
> # relax module imports.
> from lib.auto_relaxation.ri_comps import calc_fixed_csa,
> calc_fixed_dip, comp_csa_const_func, comp_dip_const_func
> from lib.physical_constants import h_bar, mu0, return_gyromagnetic_ratio
>
>
> class Data:
> """Dummy class for storing data."""
>
> # Initialise the data container.
> data = Data()
>
> # The spectrometer frequency (Hz).
> frq = 500e6
>
> # The dynamically averaged bond length (m) and chemical shift tensor
> anisotropy.
> r = 1.02e-10
> csa = -172e-6
>
> # Add the needed physical constants to the data storage.
> data.gx = return_gyromagnetic_ratio('15N')
> data.gh = return_gyromagnetic_ratio('1H')
> data.mu0 = mu0
> data.h_bar = h_bar
>
> # The number of frequencies.
> data.num_frq = 1
>
> # Initialise dipolar and CSA data structures.
> data.dip_const_fixed = 0.0
> data.csa_const_fixed = [0.0]
> data.dip_const_func = 0.0
> data.csa_const_func = zeros(1, float64)
>
> # Nuclear frequencies.
> frq = frq * 2 * pi
> frqX = frq * data.gx / data.gh
>
> # Calculate the five frequencies which cause R1, R2, and NOE relaxation.
> data.frq_list = zeros((1, 5), float64)
> data.frq_list[0, 1] = frqX
> data.frq_list[0, 2] = frq - frqX
> data.frq_list[0, 3] = frq
> data.frq_list[0, 4] = frq + frqX
> data.frq_sqrd_list = data.frq_list ** 2
>
> # Calculate the fixed component of the dipolar and CSA constants.
> calc_fixed_dip(data)
> calc_fixed_csa(data)
>
> # Calculate the dipolar and CSA constants.
> comp_dip_const_func(data, r)
> comp_csa_const_func(data, csa)
>
> # Rename the dipolar and CSA constants.
> d = data.dip_const_func
> c = data.csa_const_func[0]
>
> # Printout.
> print("d: %s" % d)
> print("c: %s" % c)
>
> --------------------------------------------------------------------------------------------------
> d: 1300116668.53
> c: 1000661534.67
>
> 2014-03-18 17:15 GMT+01:00 Edward d'Auvergne <edw...@nmr-relax.com>:
>> Hi Stefano,
>>
>> When running relax, you should avoid putting any files in the relax
>> source code directories. These should be kept separate at all times -
>> otherwise the result could be severe problems that are very difficult
>> to understand. To see the output of the script when running in GUI
>> mode, you will have to open the relax controller window were all
>> messages are displayed. To do this, perform one of:
>>
>> - Select the 'View->Controller' menu item.
>> - Click on the 'relax controller' button in the toolbar.
>> - Type Ctrl-Z.
>>
>> The two numbers should be printed at the bottom. If you see errors,
>> then there is likely to be word wrapping problems - one line has been
>> split into two in the email text.
>>
>> Regards,
>>
>> Edward
>>
>>
>> On 18 March 2014 17:06, Stefano Luciano Ciurli <stefano.ciu...@unibo.it>
>> wrote:
>>> Hi Edward,
>>> thank you for the exhaustive answer.
>>> I have saved the script as a filename.py file in the
>>> /relax/Contents/Resources/user_functions directory and tried to run in from
>>> within relax using the menu user functions (n-z) -> script
>>> However, it does not appear to do anything.
>>> Any hint?
>>> Stefano
>>>
>>> On Mar 18, 2014, at 10:04 AM, Edward d'Auvergne wrote:
>>>
>>> # Python module imports.
>>> from numpy import float64, zeros
>>>
>>> # relax module imports.
>>> from lib.auto_relaxation.ri_comps import calc_fixed_csa,
>>> calc_fixed_dip, comp_csa_const_func, comp_dip_const_func
>>> from lib.physical_constants import h_bar, mu0, return_gyromagnetic_ratio
>>>
>>>
>>> class Data:
>>> """Dummy class for storing data."""
>>>
>>> # Initialise the data container.
>>> data = Data()
>>>
>>> # The spectrometer frequency (Hz).
>>> frq = 500e6
>>>
>>> # The dynamically averaged bond length (m) and chemical shift tensor
>>> anisotropy.
>>> r = 1.02e-10
>>> csa = -172e-6
>>>
>>> # Add the needed physical constants to the data storage.
>>> data.gx = return_gyromagnetic_ratio('15N')
>>> data.gh = return_gyromagnetic_ratio('1H')
>>> data.mu0 = mu0
>>> data.h_bar = h_bar
>>>
>>> # The number of frequencies.
>>> data.num_frq = 1
>>>
>>> # Initialise dipolar and CSA data structures.
>>> data.dip_const_fixed = 0.0
>>> data.csa_const_fixed = [0.0]
>>> data.dip_const_func = 0.0
>>> data.csa_const_func = zeros(1, float64)
>>>
>>> # Nuclear frequencies.
>>> frq = frq * 2 * pi
>>> frqX = frq * data.gx / data.gh
>>>
>>> # Calculate the five frequencies which cause R1, R2, and NOE relaxation.
>>> data.frq_list = zeros((1, 5), float64)
>>> data.frq_list[0, 1] = frqX
>>> data.frq_list[0, 2] = frq - frqX
>>> data.frq_list[0, 3] = frq
>>> data.frq_list[0, 4] = frq + frqX
>>> data.frq_sqrd_list = data.frq_list ** 2
>>>
>>> # Calculate the fixed component of the dipolar and CSA constants.
>>> calc_fixed_dip(data)
>>> calc_fixed_csa(data)
>>>
>>> # Calculate the dipolar and CSA constants.
>>> comp_dip_const_func(data, r)
>>> comp_csa_const_func(data, csa)
>>>
>>> # Rename the dipolar and CSA constants.
>>> d = data.dip_const_func
>>> c = data.csa_const_func[0]
>>>
>>> # Printout.
>>> print("d: %s" % d)
>>> print("c: %s" % c)
>>>
>>
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