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Add Kehl ENDOR pulse sequences #80

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3e28cb9
Add Kehl ENDOR pulse sequences
May 8, 2026
999f5a5
Fold Kehl ENDOR options into parameters
May 8, 2026
7ac1764
Fix Kehl ENDOR orientation edge cases
May 8, 2026
9b4e27f
Use coupling eigs in Kehl ENDOR examples
May 8, 2026
1971308
Move Kehl experiment setup into context
May 8, 2026
160ecd6
Infer Kehl context data from spin system
May 8, 2026
e969423
Inline Kehl ENDOR helper stack
May 8, 2026
0b5fecd
Use Spinach constants in Kehl context
May 8, 2026
475eb22
Use Spinach isotope metadata in Kehl ENDOR
May 8, 2026
a7c4aa3
Use direct Liouville vectorisation in Kehl ENDOR
May 8, 2026
56bf93e
Use direct reshape in Kehl ENDOR
May 8, 2026
23f02e3
Restore Kehl ENDOR sequence files
May 8, 2026
f8d645f
Use Spinach operators in Kehl ENDOR kernels
May 8, 2026
332bde4
Move Kehl experiment fields into parameters
May 8, 2026
6221822
Extract Kehl context physics helpers
May 8, 2026
004a498
Use Spinach Hamiltonian assembly in Kehl ENDOR
May 8, 2026
bc6eb8b
Cache Kehl Hamiltonian orientation basis
May 8, 2026
c59238a
Harden Kehl ENDOR integration style
May 8, 2026
20a0558
Use full Spinach systems in Kehl ENDOR
May 9, 2026
fcabac9
Use Spinach relaxation in Kehl ENDOR
May 9, 2026
ee1e8b5
Run Kehl ENDOR in Zeeman Liouville space
May 9, 2026
433b63c
Port Kehl EPR selection to Liouville space
May 9, 2026
57fbfc7
Remove Kehl operator basis caches
May 9, 2026
6d713d2
Prune unused Kehl function arguments
May 9, 2026
e3d2209
Inline Kehl initial state construction
May 9, 2026
5ef6950
Normalise Kehl ENDOR units
May 9, 2026
a91344f
Refactor Kehl sequence setup and relaxation
May 9, 2026
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100 changes: 100 additions & 0 deletions examples/esr_sol_pulsed/endor_kehl_mims_powder.m
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% Exemplary setup of a 19F Mims ENDOR simulation at 34 GHz using
% Spinach constructor, ENDOR context, and pulse-sequence function style.
%
% March 2024 A. Kehl (akehl@gwdg.de)
% Spinach architecture migration May 2026 Talos

function endor_kehl_mims_powder()

% Define constants
constants=kehl_constants();

% Spinach spin-system constructor input
T=0.066;
D=6.5;

sys.magnet=1.20521;
sys.isotopes={'E','19F','1H','1H','14N'};
sys.output='hush';
sys.disable={'hygiene'};

inter.zeeman.matrix=cell(1,5);
inter.zeeman.matrix{1}=diag([2.00886,2.00610,2.00211]);
inter.zeeman.matrix{2}=local_tensor([205,310,358],[29,14,-87]);
inter.zeeman.matrix{3}=zeros(3,3);
inter.zeeman.matrix{4}=zeros(3,3);
inter.zeeman.matrix{5}=zeros(3,3);

inter.coupling.matrix=cell(5,5);
inter.coupling.matrix{1,2}=local_tensor([2*T,-T,-T]*1e6,[161,1,0]);
inter.coupling.matrix{1,5}=local_tensor([15,11,95.8]*1e6,[0,0,0]);
inter.coupling.matrix{5,5}=local_traceless_tensor([1.2,0.54,-1.7]*1e6,[0,0,0]);
inter.coupling.matrix{2,3}=local_tensor([2*D,-D,-D]*1e3,[-16.9,143.0,0]);
inter.coupling.matrix{2,4}=local_tensor([2*D,-D,-D]*1e3,[-47.9,34.3,0]);

bas.formalism='zeeman-hilb';
bas.approximation='none';

spin_system=create(sys,inter);
spin_system=basis(spin_system,bas);

% Experiment parameters
expt=kehl_exp_create(33.7727,12052.1,0.5,0.001,0.3,...
[12,2000,12,1000,200000,1000,12]);
expt=kehl_mims_fields(constants,expt,true,[0,0]);
expt=kehl_exp_freq(expt,32,3,0.001);
expt=kehl_exp_angle(expt,163);
expt=kehl_exp_pulse(expt,...
fullfile(fileparts(mfilename('fullpath')),'kehl_mlr09_12ns_pulse.txt'),false);

% Context options
values=containers.Map;
values('freqDomain')=true;
values('powder')=true;
values('Nang')=50;
values('Relax')=false;
values('Bterm')=false;
opt=kehl_set_opt([],values);

% ENDOR context metadata
parameters.inter=inter;
parameters.endor_spins=[2,3,4];
parameters.epr_spins=5;
parameters.epr_quadrupole_matrix=local_tensor([1.2,0.54,-1.7]*1e6,[0,0,0]);
parameters.n_spin_systems=1;
parameters.dipolar_pairs=[2,3;2,4];
parameters.expt=expt;
parameters.opt=opt;

% Actual ENDOR calculation through Spinach-style context and experiment
[endor_amp,endor_amp_conv,x_coords,v_L]=endor_kehl_context(spin_system,@endor_kehl_mims,parameters,'labframe'); %#ok<ASGLU>

% Plotting
sim=endor_amp(:)-endor_amp(1);
sim=sim/min(sim);
plot((x_coords(:))*1e-6,sim);

end

function T=local_traceless_tensor(values,eulers_deg)
values=values-mean(values);
T=local_tensor(values,eulers_deg);
end

function T=local_tensor(values,eulers_deg)
alpha=eulers_deg(1)*pi/180;
beta=eulers_deg(2)*pi/180;
gamm=eulers_deg(3)*pi/180;
R=zeros(3,3);
R(1,1)=cos(beta)*cos(alpha)*cos(gamm)-sin(alpha)*sin(gamm);
R(1,2)=cos(beta)*sin(alpha)*cos(gamm)+cos(alpha)*sin(gamm);
R(1,3)=-sin(beta)*cos(gamm);
R(2,1)=-cos(beta)*cos(alpha)*sin(gamm)-sin(alpha)*cos(gamm);
R(2,2)=-cos(beta)*sin(alpha)*sin(gamm)+cos(alpha)*cos(gamm);
R(2,3)=sin(beta)*sin(gamm);
R(3,1)=sin(beta)*cos(alpha);
R(3,2)=sin(beta)*sin(alpha);
R(3,3)=cos(beta);
T=R*diag(values)*R';
end

98 changes: 98 additions & 0 deletions examples/esr_sol_pulsed/endor_kehl_time_powder.m
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% Exemplary setup of a 19F time-domain ENDOR simulation at 34 GHz using
% Spinach constructor, ENDOR context, and pulse-sequence function style.
%
% March 2024 A. Kehl (akehl@gwdg.de)
% Spinach architecture migration May 2026 Talos

function endor_kehl_time_powder()

% Define constants
constants=kehl_constants();

% Spinach spin-system constructor input
T=0.066;
D=6.5;

sys.magnet=1.20521;
sys.isotopes={'E','19F','1H','1H','14N'};
sys.output='hush';
sys.disable={'hygiene'};

inter.zeeman.matrix=cell(1,5);
inter.zeeman.matrix{1}=diag([2.00886,2.00610,2.00211]);
inter.zeeman.matrix{2}=zeros(3,3);
inter.zeeman.matrix{3}=zeros(3,3);
inter.zeeman.matrix{4}=zeros(3,3);
inter.zeeman.matrix{5}=zeros(3,3);

inter.coupling.matrix=cell(5,5);
inter.coupling.matrix{1,2}=local_tensor([2*T,-T,-T]*1e6,[161,1,0]);
inter.coupling.matrix{1,5}=local_tensor([15,11,95.8]*1e6,[0,0,0]);
inter.coupling.matrix{5,5}=local_traceless_tensor([1.2,0.54,-1.7]*1e6,[0,0,0]);
inter.coupling.matrix{2,3}=local_tensor([2*D,-D,-D]*1e3,[-16.9,143.0,0]);
inter.coupling.matrix{2,4}=local_tensor([2*D,-D,-D]*1e3,[-47.9,34.3,0]);

bas.formalism='zeeman-hilb';
bas.approximation='none';

spin_system=create(sys,inter);
spin_system=basis(spin_system,bas);

% Experiment parameters
expt=kehl_exp_create(33.7727,12052.1,0.5,0.24,144.24,...
[12,1600,12,1000,6000,1000,6000,344240,12]);
expt=kehl_time_fields(constants,expt,true,[0,0]);
expt=kehl_exp_freq(expt,32,3,0.001);
expt=kehl_exp_pulse(expt,...
fullfile(fileparts(mfilename('fullpath')),'kehl_mlr09_12ns_pulse.txt'),false);

% Context options
values=containers.Map;
values('freqDomain')=true;
values('powder')=true;
values('Nang')=50;
opt=kehl_set_opt([],values);

% ENDOR context metadata
parameters.inter=inter;
parameters.endor_spins=[2,3,4];
parameters.epr_spins=5;
parameters.epr_quadrupole_matrix=local_tensor([1.2,0.54,-1.7]*1e6,[0,0,0]);
parameters.n_spin_systems=1;
parameters.dipolar_pairs=[2,3;2,4];
parameters.expt=expt;
parameters.opt=opt;
parameters.time_domain=true;

% Actual ENDOR calculation through Spinach-style context and experiment
[endor_amp,endor_amp_conv,x_coords,v_L]=endor_kehl_context(spin_system,@endor_kehl_time,parameters,'labframe'); %#ok<ASGLU>

% Plotting
sim=endor_amp(:)-endor_amp(1);
sim=sim/min(sim);
plot((x_coords(:))*1e-6,sim);

end

function T=local_traceless_tensor(values,eulers_deg)
values=values-mean(values);
T=local_tensor(values,eulers_deg);
end

function T=local_tensor(values,eulers_deg)
alpha=eulers_deg(1)*pi/180;
beta=eulers_deg(2)*pi/180;
gamm=eulers_deg(3)*pi/180;
R=zeros(3,3);
R(1,1)=cos(beta)*cos(alpha)*cos(gamm)-sin(alpha)*sin(gamm);
R(1,2)=cos(beta)*sin(alpha)*cos(gamm)+cos(alpha)*sin(gamm);
R(1,3)=-sin(beta)*cos(gamm);
R(2,1)=-cos(beta)*cos(alpha)*sin(gamm)-sin(alpha)*cos(gamm);
R(2,2)=-cos(beta)*sin(alpha)*sin(gamm)+cos(alpha)*cos(gamm);
R(2,3)=sin(beta)*sin(gamm);
R(3,1)=sin(beta)*cos(alpha);
R(3,2)=sin(beta)*sin(alpha);
R(3,3)=cos(beta);
T=R*diag(values)*R';
end

128 changes: 128 additions & 0 deletions examples/esr_sol_pulsed/kehl_mlr09_12ns_pulse.txt
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1 0 225 186
2 1 254 221
3 2 254 219
4 3 243 222
5 4 218 219
6 5 216 225
7 6 253 202
8 7 472 131
9 8 1124 -30
10 9 2074 -55
11 10 2784 49
12 11 3107 159
13 12 3190 229
14 13 3190 236
15 14 3204 213
16 15 3253 190
17 16 3297 174
18 17 3368 210
19 18 3308 296
20 19 2880 414
21 20 2055 445
22 21 1248 390
23 22 745 326
24 23 585 293
25 24 584 274
26 25 598 256
27 26 540 246
28 27 473 240
29 28 421 234
30 29 409 230
31 30 429 239
32 31 422 246
33 32 404 246
34 33 371 238
35 34 370 236
36 35 376 238
37 36 361 234
38 37 331 237
39 38 311 234
40 39 314 221
41 40 334 233
42 41 334 242
43 42 313 245
44 43 291 250
45 44 274 223
46 45 274 205
47 46 290 207
48 47 283 198
49 48 273 205
50 49 260 231
51 50 228 229
52 51 229 215
53 52 257 211
54 53 248 226
55 54 257 241
56 55 252 234
57 56 257 230
58 57 253 220
59 58 275 224
60 59 269 226
61 60 255 227
62 61 256 228
63 62 256 218
64 63 255 230
65 64 262 233
66 65 260 215
67 66 248 199
68 67 242 207
69 68 250 240
70 69 273 249
71 70 261 256
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73 72 239 227
74 73 266 226
75 74 248 210
76 75 245 227
77 76 241 226
78 77 235 222
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80 79 252 209
81 80 258 222
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90 89 208 220
91 90 203 214
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93 92 244 209
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95 94 251 201
96 95 258 206
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104 103 225 216
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119 118 254 246
120 119 241 250
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122 121 254 233
123 122 255 245
124 123 255 221
125 124 252 215
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127 126 252 228
128 127 244 219
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