rsimu ator Mrsimulator Documentation Release 0.7.0dev1 The Mrsimulator Developers Sep 20, 2021 GETTING STARTED Table of Contents i List of Figures vii List of Tables ix List of Code Blocks xi I Getting Started 3 1 Installation 5 1.1 Package dependencies.............................................5 1.2 For the users..................................................5 1.2.1 Strict Requirements..........................................5 1.2.2 Installing mrsimulator using pip...................................6 1.2.3 Building mrsimulator from the source................................7 1.2.4 Test your build............................................. 10 1.3 For developers and contributors........................................ 10 1.3.1 Make your own copy of mrsimulator on GitHub........................... 10 1.3.2 Create a development environment.................................. 11 1.3.3 Make sure git is installed on your computer............................. 11 1.3.4 Copy your fork of mrsimulator from GitHub to your computer.................. 11 1.3.5 Understanding Remotes ........................................ 12 1.3.6 Build the development version of mrsimulator............................ 12 1.3.7 Note for the developers and contributors............................... 14 2 Introduction to Spin Systems 15 2.1 Site....................................................... 15 2.2 Coupling..................................................... 16 2.3 SpinSystem................................................... 17 2.3.1 Uncoupled Spin System........................................ 17 2.3.2 Coupled Spin System......................................... 18 2.3.3 Table of Class Attributes....................................... 19 3 The Basics 23 3.1 Setting up the SpinSystem objects...................................... 23 3.2 Setting up the Method objects........................................ 24 3.3 Running simulation............................................... 26 3.4 Visualizing the dataset............................................. 26 i 4 Uncoupled Spin System: Using objects 29 4.1 Site object.................................................... 30 4.2 SpinSystem object............................................... 30 4.3 Method object................................................. 31 4.4 Simulator object................................................ 31 4.5 Running simulation............................................... 31 4.5.1 Modifying the site attributes..................................... 32 4.5.2 Modifying the rotor frequency of the method............................ 32 4.5.3 Modifying the rotor angle of the method............................... 33 4.5.4 Switching the detection channels of the method........................... 35 5 Coupled Spin System: Using objects 41 5.1 Setting up coupled SpinSystem objects.................................... 41 5.1.1 Sites................................................... 41 5.1.2 Couplings................................................ 42 5.1.3 Spin system............................................... 42 5.2 Setting up the Method objects........................................ 43 5.3 Running simulation............................................... 43 5.4 Visualizing the dataset............................................. 43 6 Configuring Simulator object 45 6.1 Number of sidebands.............................................. 46 6.2 Integration volume............................................... 47 6.3 Integration density............................................... 49 6.4 Decompose spectrum.............................................. 50 6.4.1 none ................................................... 50 6.4.2 spin_system .............................................. 50 7 mrsimulator I/O 53 7.1 Simulator object................................................ 53 7.2 Spin systems objects from Simulator class.................................. 53 7.3 Serialize simulation object from Method class as CSDM compliant file.................. 54 7.4 Serialize Simulator, SignalProcessor object to file.............................. 54 II Signal Processing (mrsimulator.SignalProcessor) 55 8 Signal Processing 57 8.1 Introduction................................................... 57 8.2 SignalProcessor class............................................ 57 8.3 Convolution................................................... 58 8.3.1 Multiple convolutions......................................... 59 8.3.2 Convolution along multiple dimensions................................ 60 8.4 Serializing the operations list......................................... 61 III Models 63 9 Czjzek distribution 65 9.1 Czjzek distribution of symmetric shielding tensors............................. 65 9.2 Czjzek distribution of symmetric quadrupolar tensors............................ 66 9.3 Mini-gallery using the Czjzek distributions.................................. 67 10 Extended Czjzek distribution 69 10.1 Extended Czjzek distribution of symmetric shielding tensors........................ 69 ii 10.2 Extended Czjzek distribution of symmetric quadrupolar tensors...................... 70 10.3 Mini-gallery using the extended Czjzek distributions............................ 71 IV Examples and Benchmarks 73 11 Simulation Examples 75 11.1 1D NMR simulation (small molecules/crystalline solids).......................... 75 11.1.1 Wollastonite, 29Si (I=1/2)....................................... 75 11.1.2 Potassium Sulfate, 33S (I=3/2).................................... 78 11.1.3 Coesite, 17O (I=5/2).......................................... 81 11.1.4 Non-coincidental Quad and CSA, 17O (I=5/2)........................... 83 11.1.5 Arbitrary spin transition (single-quantum).............................. 85 11.1.6 Arbitrary spin transition (multi-quantum).............................. 89 11.1.7 Coupled spin-1/2 (Static dipolar spectrum)............................. 92 11.1.8 Coupled spins 5/2-9/2 (Quad + J-coupling)............................. 93 11.1.9 Coupled spin-1/2 (CSA + heteronuclear dipolar + J-couplings).................. 95 11.1.10 Ethanol Revisited (1H and 13C NMR)................................ 100 11.1.11 Writing Custom methods (HahnEcho)................................ 104 11.2 1D NMR simulation (macromolecules/amorphous solids).......................... 107 11.2.1 Protein GB1, 13C and 15N (I=1/2).................................. 107 11.2.2 Amorphous material, 29Si (I=1/2).................................. 109 11.2.3 Amorphous material, 27Al (I=5/2).................................. 114 11.2.4 Czjzek distribution (Shielding and Quadrupolar).......................... 117 11.2.5 Extended Czjzek distribution (Shielding and Quadrupolar).................... 121 11.3 2D NMR simulation (Crystalline solids)................................... 126 87 11.3.1 RbNO3, Rb (I=3/2) 3QMAS.................................... 126 11.3.2 Albite, 27Al (I=5/2) 3QMAS..................................... 130 87 11.3.3 RbNO3, Rb (I=3/2) STMAS.................................... 133 87 11.3.4 Rb2SO4, Rb (I=3/2) SAS...................................... 137 87 11.3.5 Rb2CrO4, Rb (I=3/2) SAS..................................... 141 11.3.6 Coesite, 17O (I=5/2) 3QMAS..................................... 144 11.3.7 Coesite, 17O (I=5/2) DAS....................................... 146 87 11.3.8 Rb2CrO4, Rb (I=3/2) COASTER................................. 150 11.3.9 Itraconazole, 13C (I=1/2) PASS................................... 153 87 11.3.10 Rb2SO4, Rb (I=3/2) QMAT.................................... 156 11.3.11 Wollastonite, 29Si (I=1/2), MAF................................... 158 2 11.3.12 MCl2.2D2O, H (I=1) Shifting-d echo................................ 161 11.4 2D NMR simulation (Disordered/Amorphous solids)............................ 167 11.4.1 Simulating site disorder (crystalline)................................. 167 11.4.2 Czjzek distribution, 27Al (I=5/2) 3QMAS.............................. 170 12 Fitting Examples (Least Squares) 175 12.1 1D Data Fitting................................................ 175 12.1.1 29Si 1D MAS spinning sideband (CSA)............................... 175 12.1.2 31P MAS NMR of crystalline Na2PO4 (CSA)............................ 180 12.1.3 31P static NMR of crystalline Na2PO4 (CSA)............................ 186 12.1.4 13C MAS NMR of Glycine (CSA) [1940 Hz]............................. 190 12.1.5 13C MAS NMR of Glycine (CSA) [5000 Hz]............................. 194 12.1.6 13C MAS NMR of Glycine (CSA) [960 Hz]............................. 199 12.1.7 13C MAS NMR of Glycine (CSA) multi-spectra fit......................... 204 12.1.8 1D PASS/MAT sideband order cross-section............................. 210 17 12.1.9 O MAS NMR of crystalline Na2SiO3 (2nd order quad)...................... 214 12.1.10 11B MAS NMR of Lithium orthoborate crystal........................... 219 iii 12.1.11 23Na MAS NMR of Nasicon...................................... 223 12.1.12 27Al MAS NMR of YAG (1st and 2nd order Quad)......................... 227 12.1.13 2H MAS NMR of Methionine..................................... 232 12.1.14 119Sn MAS NMR of SnO....................................... 236 12.2 2D Data Fitting................................................ 241 12.2.1 13C 2D MAT NMR of L-Histidine.................................. 241 87 12.2.2 Rb 2D QMAT NMR of Rb2SO4 .................................. 246 12.2.3 17O 2D DAS NMR of Coesite..................................... 251 87 12.2.4 Rb 2D 3QMAS NMR