Deer 3p soft deer.m - Revision history

Kuprov: Update function See also links and function index membership

2026-06-06T18:35:43Z

Update function See also links and function index membership

Kuprov: Rename Arguments section heading to Parameters

2026-06-05T17:48:12Z

Rename Arguments section heading to Parameters

Kuprov: Normalise sequential blank lines

2026-04-25T11:24:25Z

Normalise sequential blank lines

Kuprov: Restore pre-bulk-edit wiki content

2026-04-05T14:48:20Z

Restore pre-bulk-edit wiki content

Kuprov: Sync syntax/arguments/outputs with current Spinach source

2026-04-05T14:05:22Z

Sync syntax/arguments/outputs with current Spinach source

Kuprov at 14:49, 18 July 2019

2019-07-18T14:49:26Z

Kuprov: /* Notes */

2019-07-18T12:58:20Z

‎Notes

Kuprov: /* Examples */

2019-07-18T12:45:58Z

‎Examples

Kuprov: /* Notes */

2019-07-14T15:46:30Z

‎Notes

Kuprov: /* Outputs */

2019-07-14T15:46:19Z

‎Outputs

@@ Line 76: / Line 76: @@
 ==See also==
-[[deer_3p_hard_echo.m]], [[deer_3p_hard_deer.m]], [[deer_analyt.m]], [[eseem.m]], [[oopeseem.m]], [[deer_4p_soft_deer.m]], [[deer_4p_soft_hole.m]], [[deer_4p_soft_diag.m]], [[deer_3p_soft_hole.m]], [[deer_3p_soft_diag.m]]
+[[deer_3p_hard_echo.m]], [[deer_3p_hard_deer.m]], [[deer_analyt.m]], [[eseem.m]], [[oopeseem.m]], [[deer_4p_soft_deer.m]], [[deer_4p_soft_hole.m]], [[deer_4p_soft_diag.m]], [[deer_3p_soft_hole.m]], [[deer_3p_soft_diag.m]], [[endor_cw.m]], [[endor_davies.m]], [[endor_mims.m]], [[endor_mims_echo.m]], [[endor_mims_ideal.m]], [[fieldsweep.m]], [[hyscore.m]], [[rapidscan.m]], [[ridme.m]], [[rydmr_exp.m]], [[sifter.m]], [[Built-in_experiments]]
 ''Version 2.4, authors: [[Ilya Kuprov]]''

@@ Line 6: / Line 6: @@
       echo_stack=deer_3p_soft_deer(spin_system,parameters,H,R,K)
-==Arguments==
+==Parameters==
        parameters.pulse_frq  - frequencies for the three

@@ Line 77: / Line 77: @@
 ==See also==
 [[deer_3p_hard_echo.m]], [[deer_3p_hard_deer.m]], [[deer_analyt.m]], [[eseem.m]], [[oopeseem.m]], [[deer_4p_soft_deer.m]], [[deer_4p_soft_hole.m]], [[deer_4p_soft_diag.m]], [[deer_3p_soft_hole.m]], [[deer_3p_soft_diag.m]]
 ''Version 2.4, authors: [[Ilya Kuprov]]''

@@ Line 1: / Line 1: @@
 {{DISPLAYTITLE:deer_3p_soft_deer.m}} __NOTOC__
 Three-pulse DEER/PELDOR pulse sequence. The sequence uses soft pulses computed with the Fokker-Planck formalism.
 ==Syntax==
-echo_stack=deer_3p_soft_deer(spin_system,parameters,H,R,K)
+     echo_stack=deer_3p_soft_deer(spin_system,parameters,H,R,K)
 ==Arguments==
-−
-parameters.pulse_frq  - frequencies for the three
+      parameters.pulse_frq  - frequencies for the three
-                            pulses, Hz
+                              pulses, Hz
-−
-    parameters.pulse_pwr  - power levels for the three
+      parameters.pulse_pwr  - power levels for the three
-                            pulses, rad/s
+                              pulses, rad/s
-−
-    parameters.pulse_dur  - durations for the three
+      parameters.pulse_dur  - durations for the three
-                            pulses, seconds
+                              pulses, seconds
-−
-    parameters.pulse_phi  - initial phases for the three
+      parameters.pulse_phi  - initial phases for the three
-                            pulses, radians
+                              pulses, radians
-−
-    parameters.pulse_rnk  - Fokker-Planck ranks for the
+      parameters.pulse_rnk  - Fokker-Planck ranks for the
-                            three pulses
+                              three pulses
-−
-    parameters.p1_p3_gap  - time between the first and the
+      parameters.p1_p3_gap  - time between the first and the
-                            third pulses, seconds
+                              third pulses, seconds
-−
-    parameters.p2_nsteps  - number of second pulse posi-
+      parameters.p2_nsteps  - number of second pulse posi-
-                            tions in the interval between
+                              tions in the interval between
-                            the first and the third pulse
+                              the first and the third pulse
-−
-    parameters.echo_time  - time to sample around the ex-
+      parameters.echo_time  - time to sample around the ex-
-                            pected echo position
+                              pected echo position
-−
-    parameters.echo_npts  - number of points in the echo
+      parameters.echo_npts  - number of points in the echo
-                            discretization
+                              discretization
-−
-    parameters.rho0       - initial state
+      parameters.rho0       - initial state
-−
-    parameters.coil       - detection state
+      parameters.coil       - detection state
-−
-    parameters.spins      - irradiated spins, normally {'E'}
+      parameters.method     - soft puse propagation method,
+                              'expv' for Krylov propagation,
-    parameters.method     - soft puse propagation method,
+                              'expm' for exponential propa-
-                            'expv' for Krylov propagation,
+                              gation, 'evolution' for Spin-
-                            'expm' for exponential propa-
+                              ach evolution function
-                            gation, 'evolution' for Spin-
      H  - Hamiltonian matrix, received from context function
-−
      R  - relaxation superoperator, received from context function
-−
      K  - kinetics superoperator, received from context function
 ==Outputs==
-echo_stack  - DEER echo stack, a matrix with p2_nsteps echoes
+    echo_stack  - DEER echo stack, a matrix with p2_nsteps echoes
                    with echo_npts points each
 ==Examples==
 A number of complete examples for two- and three-electron systems are given in examples/esr_solids folder. A good way to proceed (soft_3_pulse_deer_2e.m example file) is to look at how the pulses affect the system:
@@ Line 89: / Line 71: @@
 ==Notes==
 # For the method, start with 'expm', change to 'expv' if the calculation runs out of memory, and use 'evolution' as the last resort.
 # Simulated echoes tend to be sharp and hard to catch because simulation does not have distributions in experimental parameters. Fourier transforming the echo prior to integration is recommended.
@@ Line 95: / Line 76: @@
 ==See also==
 [[deer_3p_hard_echo.m]], [[deer_3p_hard_deer.m]], [[deer_analyt.m]], [[eseem.m]], [[oopeseem.m]], [[deer_4p_soft_deer.m]], [[deer_4p_soft_hole.m]], [[deer_4p_soft_diag.m]], [[deer_3p_soft_hole.m]], [[deer_3p_soft_diag.m]]
 ''Version 2.4, authors: [[Ilya Kuprov]]''

@@ Line 1: / Line 1: @@
 {{DISPLAYTITLE:deer_3p_soft_deer.m}} __NOTOC__
 Three-pulse DEER/PELDOR pulse sequence. The sequence uses soft pulses computed with the Fokker-Planck formalism.
 ==Syntax==
-     echo_stack=deer_3p_soft_deer(spin_system,parameters,H,R,K)
+echo_stack=deer_3p_soft_deer(spin_system,parameters,H,R,K)
 ==Arguments==
-−
-      parameters.pulse_frq  - frequencies for the three
+parameters.pulse_frq  - frequencies for the three
-                              pulses, Hz
+                            pulses, Hz
-−
-      parameters.pulse_pwr  - power levels for the three
+    parameters.pulse_pwr  - power levels for the three
-                              pulses, rad/s
+                            pulses, rad/s
-−
-      parameters.pulse_dur  - durations for the three
+    parameters.pulse_dur  - durations for the three
-                              pulses, seconds
+                            pulses, seconds
-−
-      parameters.pulse_phi  - initial phases for the three
+    parameters.pulse_phi  - initial phases for the three
-                              pulses, radians
+                            pulses, radians
-−
-      parameters.pulse_rnk  - Fokker-Planck ranks for the
+    parameters.pulse_rnk  - Fokker-Planck ranks for the
-                              three pulses
+                            three pulses
-−
-      parameters.p1_p3_gap  - time between the first and the
+    parameters.p1_p3_gap  - time between the first and the
-                              third pulses, seconds
+                            third pulses, seconds
-−
-      parameters.p2_nsteps  - number of second pulse posi-
+    parameters.p2_nsteps  - number of second pulse posi-
-                              tions in the interval between
+                            tions in the interval between
-                              the first and the third pulse
+                            the first and the third pulse
-−
-      parameters.echo_time  - time to sample around the ex-
+    parameters.echo_time  - time to sample around the ex-
-                              pected echo position
+                            pected echo position
-−
-      parameters.echo_npts  - number of points in the echo
+    parameters.echo_npts  - number of points in the echo
-                              discretization
+                            discretization
-−
-      parameters.rho0       - initial state
+    parameters.rho0       - initial state
-−
-      parameters.coil       - detection state
+    parameters.coil       - detection state
-−
-      parameters.method     - soft puse propagation method,
+    parameters.spins      - irradiated spins, normally {'E'}
-                              'expv' for Krylov propagation,
-                              'expm' for exponential propa-
+    parameters.method     - soft puse propagation method,
-                              gation, 'evolution' for Spin-
+                            'expv' for Krylov propagation,
-                              ach evolution function
+                            'expm' for exponential propa-
+                            gation, 'evolution' for Spin-
      H  - Hamiltonian matrix, received from context function
-−
      R  - relaxation superoperator, received from context function
-−
      K  - kinetics superoperator, received from context function
 ==Outputs==
-    echo_stack  - DEER echo stack, a matrix with p2_nsteps echoes
+echo_stack  - DEER echo stack, a matrix with p2_nsteps echoes
                    with echo_npts points each
 ==Examples==
 A number of complete examples for two- and three-electron systems are given in examples/esr_solids folder. A good way to proceed (soft_3_pulse_deer_2e.m example file) is to look at how the pulses affect the system:
@@ Line 71: / Line 89: @@
 ==Notes==
 # For the method, start with 'expm', change to 'expv' if the calculation runs out of memory, and use 'evolution' as the last resort.
 # Simulated echoes tend to be sharp and hard to catch because simulation does not have distributions in experimental parameters. Fourier transforming the echo prior to integration is recommended.
@@ Line 76: / Line 95: @@
 ==See also==
 [[deer_3p_hard_echo.m]], [[deer_3p_hard_deer.m]], [[deer_analyt.m]], [[eseem.m]], [[oopeseem.m]], [[deer_4p_soft_deer.m]], [[deer_4p_soft_hole.m]], [[deer_4p_soft_diag.m]], [[deer_3p_soft_hole.m]], [[deer_3p_soft_diag.m]]
 ''Version 2.4, authors: [[Ilya Kuprov]]''

@@ Line 62: / Line 62: @@
 [[File:pulse_effect.png]]
-then to take a look at the echo and its Fourier transform:
+then to inspect the echo stack as a function of the pump pulse position:
-[[File:deer_echo.png]]
+[[File:deer_echo_stack.png]]
-and finally at the real and imaginary parts of the DEER trace:
+and finally to inspect the principal components of the echo stack. The most prominent component is the DEER trace, the other components come from the finite size of the spherical integration grid.
-[[File:deer_trace.png]]
+[[File:deer_echo.png]] [[File:deer_trace.png]]
 ==Notes==