Author Topic: MAS DNP capabilities  (Read 1211 times)

Fperras

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MAS DNP capabilities
« on: November 02, 2015, 06:34:58 PM »
Hello,

I was wondering if it is currently possible to simulate MAS DNP using spinach.  Simply adding MAS to the existing examples does not produce any changes in the calculated result.  If it us possible to run these simulations can the build-up curves also be simulated?  Thank you for your time.

kuprov

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Re: MAS DNP capabilities
« Reply #1 on: November 03, 2015, 09:25:35 AM »
Yes, it should work. Can I take a look at your code? It's probably something simple that's missing.

Fperras

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Re: MAS DNP capabilities
« Reply #2 on: November 05, 2015, 02:33:24 PM »
I am not that familiar with how to prepare Spinach input files, I simply added MAS to the cross-effect field scan example (and changed some of the parameters).

Code: [Select]
% Magnetic field sweep DNP experiment -- returns equilibrium population of
% the user-specified states (relative to their Boltzmann population at the
% same temperature) as a function of the applied magnetic field.
%
% Note: the default proximity cut-off in Spinach is 4 Angstroms - this
%       needs to be increased if long-range interactions are involved.
%
% Note: the calculation takes about 15 minutes because a powder average
%       is computed.
%
% i.kuprov@soton.ac.uk


%load the spinach libraries

addpath('/home/fperras/spinach_1.6.2782')
addpath('/home/fperras/spinach_1.6.2782/kernel')
addpath('/home/fperras/spinach_1.6.2782/kernel/cache')
addpath('/home/fperras/spinach_1.6.2782/kernel/external')
addpath('/home/fperras/spinach_1.6.2782/kernel/grids')
addpath('/home/fperras/spinach_1.6.2782/kernel/optimal_control')
addpath('/home/fperras/spinach_1.6.2782/kernel/overloads')
addpath('/home/fperras/spinach_1.6.2782/kernel/overloads/@cell')
addpath('/home/fperras/spinach_1.6.2782/kernel/overloads/@struct')
addpath('/home/fperras/spinach_1.6.2782/kernel/overloads/@ttclass')
addpath('/home/fperras/spinach_1.6.2782/kernel/pulse_shapes')
addpath('/home/fperras/spinach_1.6.2782/kernel/utilities')
addpath('/home/fperras/spinach_1.6.2782/etc')
addpath('/home/fperras/spinach_1.6.2782/experiments')
%end of spinach loading


function cross_effect_field_scan_1()

% Magnetic field
sys.magnet=9.4;

% Spin system
sys.isotopes={'E','E','1H'};

% Electron g-tensors
inter.zeeman.eigs=cell(3,1);
inter.zeeman.euler=cell(3,1);
inter.zeeman.eigs{1}=[2.0085 2.00605 2.00215];
inter.zeeman.euler{1}=[pi/2 0 0];
inter.zeeman.eigs{2}=[2.0085 2.00605 2.00215];
inter.zeeman.euler{2}=[0 0 0];

% 14N quadrupolar tensor
%inter.coupling.eigs=cell(4,4);
%inter.coupling.euler=cell(4,4);
%inter.coupling.eigs{3,3}=[-1e6 -1e6 2e6];
%inter.coupling.euler{3,3}=[0 0 0];

% Coordinates
inter.coordinates={[ 0.00   0.00   0.00];
                   [11.00   0.00   0.00];
%                   []                      % 14N hyperfine specified below
                   [ 5.5    1.0    0.0]};
               
% Hyperfine couplings
%inter.coupling.eigs{1,3}=[17.4e6 17.6e6 102e6];
%inter.coupling.euler{1,3}=[0 0 0];

% Exchange coupling
inter.coupling.scalar=cell(3,3);
inter.coupling.scalar{1,2}=2*(20e6);

% Proximity cutoff
sys.tols.prox_cutoff=Inf;

% Basis set
bas.formalism='sphten-liouv';
bas.approximation='none';

% Relaxation theory
inter.relaxation='t1_t2';
inter.r1_rates=[2e4 2e4 0.1];
inter.r2_rates=[7e5 7e5 10];
inter.temperature=100;

% Spinach housekeeping
spin_system=create(sys,inter);
spin_system=basis(spin_system,bas);

% MAS parameters
parameters.rate=6000;
parameters.axis=[1 1 1];
parameters.max_rank=5;
parameters.decouple={};
parameters.rframes={};
parameters.order='powder';

% Sequence parameters
parameters.mw_pwr=10e6;
parameters.mw_frq=263.5e9;
parameters.fields=linspace(9.30,9.5,500);
parameters.coil=state(spin_system,'Lz','1H');
parameters.mw_oper=(operator(spin_system,'L-','E')+...
                    operator(spin_system,'L+','E'))/4;
parameters.ez_oper=operator(spin_system,'Lz','E');
parameters.rlx_unt=relaxation(spin_system);
parameters.grid='repulsion_ab_400_sph';

% Thermal equilibrium state
[H,Q]=hamiltonian(assume(spin_system,'labframe'),'left');
parameters.rho_eq=equilibrium(spin_system,H,Q,[0 0 0]);

% Steady state simulation
answer=powder(spin_system,@dnp_field_scan,parameters,'esr');

% Plotting
%plot(parameters.fields,real(answer)); axis('tight');
%xlabel('Magnetic field, Tesla');
%ylabel('1H signal amplitude, a.u.');

xlswrite('fields.txt',parameters.fields);
xlswrite('enhancements.txt',real(answer));

end
« Last Edit: November 05, 2015, 03:53:33 PM by Fperras »

kuprov

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Re: MAS DNP capabilities
« Reply #3 on: November 15, 2015, 03:14:52 PM »
Replace "powder" with a magic angle spinning wrapper.