6-circle geometry modes
sixc configuration of spec operates a standard six-circle diffractometer. The six-circle diffractometer combines the features of a four-circle and a z-axis diffractometer.
The standard six-circle motor names and mnemonics are as follows:
|Delta||del||- Detector arm rotation|
|Theta||th||- Rotates sample circles|
|Chi||chi||- Sample tilt|
|Phi||phi||- Sample rotation|
|Mu||mu||- Diffractometer rotation|
|Gamma||gam||- Out-of-plane detector rotation|
The following optional motors select among various pseudomotor configurations (see the following section on pseudomotors).
|GamTran||gamT||- Translation component of gam|
|GamRot||gamR||- Rotation component of gam|
|GamScrew||gamS||- Screw displacement for gam|
|MuTran||muT||- Translation component of mu|
|MuRot||muR||- Rotation component of mu|
Two configurations of the diffractometer are available. At synchrotrons, the configuration is dictated by the layout of the experimental hutch with respect to the incident X rays. The setconfig macro selects the configuration. The differences between the configurations are described further down, as is the rotation sense and zero position of each circle.
The six-circle modes represent various constraints that can be made on the transformation equations from reciprocal space to diffractometer angles. Use the setmode macro to select a six-circle mode. The modes are as follows:
0 - Omega fixed (mu = gamma = 0, traditional four circle)1 - Phi fixed (mu = gamma = 0, traditional four circle)2 - Zone (mu = gamma = 0, traditional four circle)3 - Azimuth, mu and gamma fixed4 - Alpha, mu and gamma fixed5 - Beta, mu and gamma fixed6 - Azimuth and gamma fixed, mu varies7 - Alpha and gamma fixed, mu varies8 - Beta and gamma fixed, mu varies9 - Azimuth and mu fixed, gamma varies10 - Alpha and mu fixed, gamma varies11 - Beta and mu fixed, gamma varies12 - Z-Axis with azimuth fixed, chi, phi set to -sigma, -tau13 - Z-Axis with alpha fixed, chi, phi set to -sigma, -tau14 - Z-Axis with beta fixed, chi, phi set to -sigma, -tau15 - Specular with theta = 90, gamma = 0 and phi fixed16 - Chi, phi and mu fixed
In the azimuth-fixed modes (3, 6, 9 and 12), when the azimuthal angle is set to 90 degrees, the incident angle alpha will be equal to the exit angle beta.
In the z-axis modes, use the sigtau macro to calculate the azimuthal reference vector from the chi and phi angles used to align the sample.
Each of the six-circle modes has associated an angle (or angles) that are fixed in that mode. As a convenience, there is a freeze macro that turns on spec's frozen mode. When in frozen mode, all moves that specify reciprocal space coordinates will use the frozen value(s) of the current mode's fixed angle(s). Thus you can move motors around for lining up, etc., but have the the fixed angle(s) automatically restored to the frozen value when doing reciprocal space scans, br moves, etc. The unfreeze macro turns frozen mode off.
The frozen values are stored in variables (actually macros) named F_OMEGA (omega-fixed mode), F_CHI_Z and F_PHI_Z (zone mode), F_PHI (phi-fixed modes), F_CHI (chi-fixed modes), F_AZIMUTH (azimuth-fixed modes), F_ALPHA (alpha-fixed modes), F_BETA (beta-fixed modes), F_MU (mu-fixed modes) and F_GAMMA (gamma-fixed modes). You can assign values to these variables by hand, or you can pass the values as arguments to the freeze macro. For example, if you are in mode 4 (azimuth, mu and gamma fixed), typing
freeze 90 0 10
will set F_AZIMUTH to 90 degrees F_MU to zero and F_GAMMA to 10 degrees. Without arguments, the freeze macro freezes the corresponding angles at their current values.
(The six-circle sector code is still in development.)
Cut points affect the direction the diffractometer circles turn to get from one position to the next. For example, if a cut point is at zero, the corresponding circle will only move through angles of 0 to 360 degrees. Thus, to get from 355 (=-5) to 5 degrees, the circle will turn 350 degrees. If a cut point is at -180, the circle will move through angles from -180 to 180. Thus the same motion from -5 to 5 will require only 10 degrees of movement. Use the cuts macro to select cut points for theta, chi and phi (and the azimuth). The delta, mu and gamma motors always use -180 as the cut point. (Only the sign of the azimuth cut point is used, and it determines the sign of the azimuth angle.)
The setlat and setrlat macros let you set the lattice parameters in direct space or reciprocal space, respectively.
With known lattice parameters, you need to find two (nonparallel) reflections in order to determine the orientation matrix. The macros or0 H K L and or1 H K L are used to associate the current diffractometer angles with the primary and secondary reflections. Macros called setor0 and setor1 also let you set the orientation reflections, but don't require you to move the diffractometer to the correct position. Instead, you are prompted for each of the angles and values for H, K and L. The or_swap macro is available to exchange the primary and secondary reflections.
You can also fit an orientation matrix if you have three or more known reflections (not all in the same plane), but unknown lattice parameters. Use reflex_beg to initialize a reflections data file. Use reflex H K L to add the current reflection to the file. Use reflex_end to complete the file. You then run the reflections file as a spec command file in order to fit the reflections to obtain a new orientation matrix. To calculate lattice parameters from the new orientation matrix, type calcL. You can then display the lattice parameters with the pa macro. You can edit the reflections file to delete or modify any of the reflection data there.
spec supports configurations where the gamma detector rotation and/or the mu diffractometer rotation involves multiple motors or is done indirectly.
In one gamma configuration, the detector is mounted on a small rotation stage that tracks the desired gamma angle. Another motor translates that stage to keep the detector oriented towards the sample. That configuration is selected by configuring two motors having mnemonics gamR and gamT in the config file.
In another gamma configuration, the rotation is created by translating the detector along a curved track using a linear screw pivoted at one end. The screw motor must have the mnemonic gamS. In both configurations, a motor with mnemonic gam must also be configured, but with the controller set to NONE.
In yet another configuration, the mu rotation is made up of a rotation and a translation, just as described for gamma, above. This configuration is selected when there are motors having mnemonics muR and muT in the config file. The motor configured as mu must have the controller type set to NONE.
In normal operation, a "tracking" mode is on such that commands to move the pseudomotors gam or mu are automatically converted to motions of the associated real motors, and the positions of the pseudomotors are calculated based on the positions of the real motors. With "tracking" mode off, the real motors will be unconnected from their associated pseudomotor. Commands to move the pseudomotors won't affect the real motors, and the real motor positions won't change the value of the pseudomotors. "Tracking" mode is stored in g_track. The ontrack, offtrack and settrack macros can be used to set g_track. The "tracking" macros will apply to both gamma and mu pseudomotors together.
(The mu pseudomotor was added in spec release 5.10.01-6.)
GLOBALS AND MACROS
a built-in array which holds the following six-circle parameters:
- def H 'Q'
- Reciprocal space coordinate.
- def K 'Q'
- Reciprocal space coordinate.
- def L 'Q'
- Reciprocal space coordinate.
- def LAMBDA 'Q'
- Wavelength of X rays.
- def ALPHA 'Q'
- Incident angle, useful for surface diffraction.
- def BETA 'Q'
- Exit angle, useful for surface diffraction.
- def OMEGA 'Q'
- The theta - two-theta / 2 parameter.
- def TTH 'Q'
- The Bragg angle.
- def AZIMUTH 'Q'
- Rotation angle of a reference vector about the scattering vector, useful for surface diffraction.
- def SIGMA 'Q'
- With TAU, an alternative description of the azimuthal reference vector.
- def TAU 'Q'
- With SIGMA, an alternative description of the azimuthal reference vector.
- def F_ALPHA 'Q'
- Frozen value of ALPHA for alpha-fixed mode.
- def F_BETA 'Q'
- Frozen value of BETA for beta-fixed mode.
- def F_OMEGA 'Q'
- Frozen value of OMEGA for omega-fixed mode.
- def F_AZIMUTH 'Q'
- Frozen value of AZIMUTH for azimuth-fixed mode.
- def F_PHI 'Q'
- Frozen value of A[phi] for phi-fixed modes.
- def F_CHI_Z 'Q'
- Frozen value of A[chi] for zone mode.
- def F_PHI_Z 'Q'
- Frozen value of A[phi] for zone mode.
- def F_MU 'Q'
- Frozen value of A[mu] for mu-fixed modes.
- def F_GAMMA 'Q'
- Frozen value of A[gam] for gamma-fixed modes.
- def CUT_AZI 'Q'
- The azimuth cut point flag.
- def CUT_DEL 'Q'
- The delta cut point.
- def CUT_TH 'Q'
- The theta cut point.
- def CUT_CHI 'Q'
- The chi cut point.
- def CUT_PHI 'Q'
- The phi cut point.
- def CUT_MU 'Q'
- The mu cut point.
- def CUT_GAM 'Q'
- The gamma cut point.
- def F_CHI 'Q'
- Frozen value of A[chi] for chi-fixed, phi-fixed, mu-fixed mode.
a built-in array which holds the following six-circle parameters:
- def g_mode 'G'
- Holds current six-circle mode.
- def g_sect 'G'
- Holds current six-circle sector.
- def g_frz 'G'
- Nonzero when frozen mode is on.
- def g_haz 'G'
- H of azimuthal reference vector.
- def g_kaz 'G'
- K of azimuthal reference vector.
- def g_laz 'G'
- L of azimuthal reference vector.
- def g_zh0 'G'
- H of first zone-mode vector.
- def g_zk0 'G'
- K of first zone-mode vector.
- def g_zl0 'G'
- L of first zone-mode vector.
- def g_zh1 'G'
- H of second zone-mode vector.
- def g_zk1 'G'
- K of second zone-mode vector.
- def g_zl1 'G'
- L of second zone-mode vector.
- def g_len 'G'
- When using either of the gamma-pseudomotor configurations, the distance from the sample to the gamma stage when gamma = 0.
- def g_config 'G'
- If zero, the default configuration is selected. Otherwise, the alternate configuration is used.
- def g_track 'G'
- If nonzero, the gamT and gamR motors track the pseudomotor gam. Must be set to zero to move gamT and gamR directly.
- def g_sigtau 'G'
- If nonzero, SIGMA and TAU are considered fundamental and the azimuthal reference vector is calculated from their values. Otherwise SIGMA and TAU are calculated from the azimuthal reference vector. Use the setconfig macro to change the value of g_sigtau.
- def g_len2 'G'
- When using the screw gamma-pseudomotor configuration, the distance from the screw pivot point to the gamma stage when gamma = 0.
- calculates H, K, L, ALPHA, BETA, AZIMUTH, TTH, OMEGA, SIGMA and TAU from the six-circle angles in the motor array A.
- calculates A, OMEGA, ALPHA, BETA and AZIMUTH from H, K and L.
- calculates the phi and chi to put the two vectors specified by the six elements of the built-in Z array in the scattering plane.
- cz H0 K0 L0 H1 K1 L1
- "calculate zone", prints the chi and phi necessary to put the two vectors specified as arguments in the scattering plane.
- mz H0 K0 L0 H1 K1 L1
- "move zone", moves to the chi and phi values that put the two vectors specified as arguments into the scattering plane. Also sets zone mode and turns on frozen mode using the calculated chi and phi values.
- sz H0 K0 L0 H1 K1 L1
- "set zone", calculates the chi and phi values that put the two vectors specified as arguments into the scattering plane. Also sets zone mode and turns on frozen mode using the calculated chi and phi values.
- setaz [H K L]
- Sets the azimuthal reference vector.
- sigtau [sigma tau]
- Sets the azimuthal reference vector according to the angles given as arguments. If no arguments are given, the macro will prompt for sigma and tau, using the negative of the current values of chi and phi, respectively, as the defaults.
- Displays the current geometry parameters.
- Prompts for the various geometry parameters.
- setlen [length]
- Prompts for the delta-arm length needed for the gamma-pseudomotor calculations.
- setconfig [which]
- Prompts for the configuration. Zero selects the z-outward configuration. Nonzero selects the z-inward configuration.
- settrack [1|0]
- Sets the value of g_track to the argument, if any, otherwise prompts for a value.
- equivalent to settrack 1.
- equivalent to settrack 0.
- aziscan start finish intervals time
- Does a scan of the azimuthal angle.
ZEROS AND ROTATION SENSE
For the two supported diffractometer configurations, the x axis points upward and the y axis points along the direction of the incident beam. The two configurations are mirror images of each other in the x-y plane, but both use a right-handed coordinate system. When all circle are at zero, the default configuration (g_config = 0) has the z axis pointing outward from a sample mounted on the phi circle. In the alternate configuration (g_config != 0), the z axis points inward. The choice of configuration is generally dictated by the the dimensions and layout of a synchrotron hutch.
In order for the calculations in the six-circle code to work correctly, you must set the rotation sense and zeros of the circles according to the conventions built into the code. The rotation sense is defined with respect to the positive unit vectors of the laboratory coordinate system described above. For a right-handed rotation, if your thumb points along the unit vector that is in line with the rotation axis, your fingers will point in the positive rotation direction.
The rotation sense of an axis can be changed by changing the sign of the steps-per-degree parameter or the sign-of-user*dial parameter in the config file. You should set the sign of the first parameter so that the spec dial positions agree with the dial indicators of each circle. Set the sign of the second parameter as necessary to make the spec user angles agree with the rotation sense described below.
In the default (z-outward) configuration, the mu circle is in the y-z plane, with the rotation axis along the x axis with a right-handed rotation convention. The zero of mu is such that the delta and theta circles are on the negative side of the x-y plane with their rotation axes along the z axis.
The delta, theta and phi circles all have a left-handed rotation sense. The delta circle is at zero when the detector arm is along the negative y direction. Theta is zero when the chi circle is in the x-z plane, with the chi axis along the y axis. The chi rotation is right-handed. The zero of chi puts the phi rotation axis along the z direction with the "surface normal" of the phi table pointed in the positive z direction. The zero of the phi circle is arbitrary.
Finally, with mu and delta at zero, the gamma circle is located in the y-z plane with the zero of gamma chosen so that the detector is pointed in the negative y direction towards the X-ray source. The gamma rotation is right handed.
In the alternate, mirror image, z-inward configuration, all rotations are left handed.
Angle calculations and operating modes for a six-circle diffractometer were presented by M. Lohmeier and E. Vlieg in J. Appl. Cryst., 26, 706 (1993). (See http://journals.iucr.org/j/issues/1993/05/00/la0044.)
Extensions, including explicit formulas for the setting of diffractometer motors based on the surface normal direction, were given by D. Abernathy (PhD thesis, MIT 1993), who also assisted in developing the C code used in spec.