Spin system specification - Revision history

Kuprov: Document the inter.modes bosonic mode input block (Spinach 2.12, PR 195)

2026-08-06T04:43:51Z

Document the inter.modes bosonic mode input block (Spinach 2.12, PR 195)

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Kuprov: Normalise sequential blank lines

2026-04-25T11:30:00Z

Normalise sequential blank lines

Kuprov: /* Isotopes and text labels */

2024-05-08T16:21:17Z

‎Isotopes and text labels

Kuprov: /* Isotopes and text labels */

2024-05-08T16:21:03Z

‎Isotopes and text labels

Kuprov: /* Isotopes and text labels */

2024-05-08T12:45:17Z

‎Isotopes and text labels

Kuprov: /* SIMPSON import */

2023-11-03T14:18:32Z

‎SIMPSON import

Kuprov: /* Tolerances and algorithm switches */

2023-07-29T12:26:49Z

‎Tolerances and algorithm switches

Kuprov: /* Liquid crystal order matrix */

2023-07-29T10:53:23Z

‎Liquid crystal order matrix

Kuprov: /* SIMPSON import */

2023-07-28T10:28:42Z

‎SIMPSON import

Kuprov: /* SIMPSON import */

2023-07-28T10:28:29Z

‎SIMPSON import

← Older revision		Revision as of 11:30, 25 April 2026
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	On suitable hardware (solid state disks, NVidia Tesla cards), these options can significantly improve performance. See the [[Appendix_F:_expert-level_options\|expert level options]] page for further information.		On suitable hardware (solid state disks, NVidia Tesla cards), these options can significantly improve performance. See the [[Appendix_F:_expert-level_options\|expert level options]] page for further information.
−

	''Version 2.8, authors: [[Ilya Kuprov]], [[Luke Edwards]], [[Hannah Hogben]]''		''Version 2.8, authors: [[Ilya Kuprov]], [[Luke Edwards]], [[Hannah Hogben]]''

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 An electron may be selected by specifying 'E'. Electron shells with multiplicity higher than 2 may be selected by specifying a multiplicity after the electron label, e.g. 'E3' requests a spin-1 electron. All known isotopes are supported, you can specify your own particles by editing the [[spin.m]] file in the kernel.
-''Spinach'' supports particles of any spin, including spin zero. Spin zero particles only have the unit state – they do not influence matrix dimension and all couplings to them are effectively ignored. To request a spin zero particle, simply specify the corresponding isotope, for example '12C'.
+''Spinach'' supports particles of any spin, including spin zero. Spin zero particles only have the unit state – they do not influence matrix dimension and all couplings to them are effectively ignored. To request a spin zero particle, simply specify the corresponding isotope, for example '12C'. ''Spinach'' also has a spin-zero "ghost" particle built in. A ghost particle does not participate in any dynamics and may be specified using 'G'.
 There is experimental support for cavity and phonon modes. Use 'C#' and 'V#' notation, for example 'C10' requests a cavity mode with 10 population number levels.

@@ Line 12: / Line 12: @@
 An electron may be selected by specifying 'E'. Electron shells with multiplicity higher than 2 may be selected by specifying a multiplicity after the electron label, e.g. 'E3' requests a spin-1 electron. All known isotopes are supported, you can specify your own particles by editing the [[spin.m]] file in the kernel.
 ''Spinach'' supports particles of any spin, including spin zero. Spin zero particles only have the unit state – they do not influence matrix dimension and all couplings to them are effectively ignored. To request a spin zero particle, simply specify the corresponding isotope, for example '12C'.
 ''Spinach'' also has a spin-zero "ghost" particle built in. A ghost particle does not participate in any dynamics and may be specified using 'G'.
 Optionally, specify a label for each spin by giving a list of strings, for example:

← Older revision		Revision as of 12:45, 8 May 2024
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	Labels are printed next to spin interaction summaries – this makes them easier to read for large spin systems. When they are unique, labels may be used (via [[idxof.m]] function) to refer to spins by their labels. Labels are also used by protein NMR spectroscopy modules to identify different types of atoms – when a dedicated protein pulse sequence (such as [[hncoca.m]]) is run, these labels must be set to the standard PDB atom identifiers. If this field is omitted, all labels are set to empty strings. PDB and BMRB import function [[protein.m]] sets these labels automatically.		Labels are printed next to spin interaction summaries – this makes them easier to read for large spin systems. When they are unique, labels may be used (via [[idxof.m]] function) to refer to spins by their labels. Labels are also used by protein NMR spectroscopy modules to identify different types of atoms – when a dedicated protein pulse sequence (such as [[hncoca.m]]) is run, these labels must be set to the standard PDB atom identifiers. If this field is omitted, all labels are set to empty strings. PDB and BMRB import function [[protein.m]] sets these labels automatically.
		+
		+	To make isotope replacements in existing [[sys]] and [[inter]] data structures, use [[isoswap.m]] function.

	==Zeeman interactions==		==Zeeman interactions==

← Older revision		Revision as of 14:18, 3 November 2023
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	To verify the chemical shifts after the import and a call to [[create.m]], either inspect the console output, or use [[chemshifts.m]] function. Imports from multiple electronic structure theory calculations may be merged using [[merge_inp.m]] function.		To verify the chemical shifts after the import and a call to [[create.m]], either inspect the console output, or use [[chemshifts.m]] function. Imports from multiple electronic structure theory calculations may be merged using [[merge_inp.m]] function.
−
−	~~==SIMPSON import==~~
−	~~Spin system information may also be read from the spinsys{} field of a SIMPSON *.in file using the following syntax:~~
−
−	~~<nowiki>[</nowiki>[[sys]],[[inter]]]=[[s2spinach.m\|s2spinach]](filename);~~
−
−	The function absorbs isotope information, all Zeeman tensors and all coupling tensors, and returns ''Spinach'' [[sys]] and [[inter]] data structures with that information. Structures from multiple imports may be merged using [[merge_inp.m]] function.

	==Protein and nucleic acid import==		==Protein and nucleic acid import==

← Older revision		Revision as of 12:26, 29 July 2023
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−	''Version 2.1, authors: [[Ilya Kuprov]], [[Luke Edwards]], [[Hannah Hogben]]''	+	''Version 2.8, authors: [[Ilya Kuprov]], [[Luke Edwards]], [[Hannah Hogben]]''

@@ Line 174: / Line 174: @@
 ==Liquid crystal order matrix==
-For partially oriented systems, the 3x3 Saupe order matrix may be supplied to enable the simulation of residual dipolar couplings, residual quadrupolar couplings and orientational residuals of all other anisotropic interactions in your system - everything you have specified will be processed. Order matrix specification example with typical values for dilute liquid crystals at room temperature:
+For partially oriented systems, the 3x3 Saupe order matrices (one per chemical component, as a cell array of 3x3 matrices) may be supplied to enable the simulation of residual dipolar couplings, residual quadrupolar couplings, and orientational residuals of any other anisotropic interactions in your system. Order matrix specification example with typical values for dilute liquid crystals at room temperature:
-      [[inter]].order_matrix=diag([1e-3 2e-3 -3e-3]);
+      [[inter]].order_matrix={diag([1e-3 2e-3 -3e-3])};
 At simulation time, the transformation of interaction tensors into their partially averaged from is handled by [[liquid.m]] context function. It may be performed manually by calling [[residual.m]] function.

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       <nowiki>[</nowiki>[[sys]],[[inter]]]=[[s2spinach.m|s2spinach]](filename);
-The function absorbs isotope information, all Zeeman tensors and all coupling tensors, and returns ''Spinach'' [[sys]] and [[inter]] data structures with that information. Structures from multiple imports may be merged using merge_inp.m function.
+The function absorbs isotope information, all Zeeman tensors and all coupling tensors, and returns ''Spinach'' [[sys]] and [[inter]] data structures with that information. Structures from multiple imports may be merged using [[merge_inp.m]] function.
 ==Protein and nucleic acid import==