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C. Calculating and using simulated spectra Select the SIMULATION dialog from the MAIN MENU. The ROTOR CALCULATION OPTIONS DIALOG will be displayed. Depress the READ FILE button in the INPUT FLNM section and click on the file, 1fnMW.in. This is the input file to the rotor program, iar95.exe. Seethe document, iar95UserGuide.wpd, for a more detailed description of this file. Select YES when prompted with the question, COPY PARAMETERS TO CAL/FIT VALUES?. All parameter option fields will be filled in. Descriptions for each of the parameter fields are given in the following paragraphs. CALC CUTOFF PARAMETERS section: Enter the maximum J (J MAX) to calculate, the transition intensity cutoff (ITN CUT)and the rotational temperature (TEMP (K)). The rotational temperature specified in Kelvin is converted to frequency (energy) in units of MHz so convert the temperature to agree with the units used to specify the rotational constants. LINEAR LEAST SQUARES section: Enter the assignment filename (ASN FLNM), typically having a ASN extension. If this file exists, the number of assignments will appear under the ASN LINES heading. For predicting spectra, set the LSF CYCS to 0. Otherwise, the rotor program will attempt to do a least squares fit of the parameters to the assigned line set if greater than 0. The program will fail, of course, if there are no assigned lines. The rejection level (REJ LEVEL) parameter will be used to remove assigned lines from the fit when the difference in the assigned and calculated frequencies exceed this value. During initial fitting stages when large changes in the parameters are expected, this number should be fairly large. Also note that for least-squares fits, all assigned lines that satisfy the rejection level condition will be included in the fit regardless of band type and/or quantum number. ROTATIONAL CONSTANT section: Two sets of values are given for each rotational constant. The first column of parameters with the heading FILE I/O are always the values read from and written to the input file. The values of the asymmetry parameter, (KAPPA) and the inertial defect, I (DELTA I) are also calculated using these values. The second column under the heading CALC/FIT contains the initial set of parameters used by the rotor program for predicting or fitting spectra. The check boxes under the heading VAR STAT enable the variation of the parameter when performing linear least-squares fits using the rotor program. The ORIGIN parameter has special meaning when set to exactly zero. In this case, the upper state constants are ignored and derivatives for least squares fits are generated in order to fit pure rotational spectra for the lower state only. Both states are used in the calculation for origin values greater than or equal to 0.000001. (This meaning will change in a future release.) Selecting the NON-RR PARA button brings up the NON-RIGID ROTORPERTURBATION OPTIONS DIALOG. This dialog provides access to Coriolis coupling parameters, Watson's centrifugal distortion (A reduction in the IR representation) and the Euler angles for inertial axis reorientation in each state. See the document, iar95UserGuide.wpd, for a complete description of the sign conventions used. TM/DIPOLE section: Under the CALC heading, set the percentages of the transition moment components squared (TM) or dipole moment intensity desired along each of the principle axes. The magnitude of the calculated components may be reduced in magnitude by using the TM/DIPOLE ADJUSTMENT DIALOG from the MAIN WINDOW display (vide infra). IAR CALCULATION section: The rotor program, iar95.exe, will be executed upon depressing the RUN button. For a detailed description of the rotor program, see the iar95UserGuide.wpd. The path to the executable, iar95.exe, is automatically set according to the following upon selecting SIMULATION option from the MAIN WINDOW. If the file, jb95.dir, exists in the parent directory of the working folder, the first line of this file is read to set the path. If this file does not exist, the path to the jb95.exe executable is used. When the rotor program is run, a generic inputfile IAR.in is written and the rotor program appears in a console mode (DOS) box. After the program finishes (DOS box disappears), depress the READ button to read the generic binary output file (.p) for the rotational constants, standard uncertainties (i.e., standard deviation, 1),number of calculated and assigned lines and the observed-minus-calculated standard deviation of the line set. Checking the SIMS box, brings up SIMULATION CONTROL DIALOG. SIMULATION CONTROL DIALOG: In order to view the simulated line set generated using iar95.exe, the generic set of files(containing the IAR prefix) must be moved into one of the nine simulation channels given in the SIMULATION CONTROL DIALOG. Access to this dialog is provided by using either the hotkey c or the RIGHT CLICK menu option from the MAIN WINDOW display. Both options actually toggle on/off the display status of this dialog. Also notice that this dialog is modelessand therefore, may remain active while performing other functions from the MAIN WINDOW display or from other modal dialogs. SIMULATIONS section: Select one of the nine simulation channels using the horizontal scroll list control. Enter a filename (1fnMW in this example) in the FILE NAME field. Depress the RD IAR button to rename the generic files to this base filename with appropriate extensions added. If the files already exist, you will be prompted to overwrite them. The calculated spectrum should appear in the MAIN WINDOW display upon checking the DSP STAT box. To add together intensities from more than one simulation channel, first display the simulations and then check the SUM boxes for those channels. The waveform of the co-added simulations will appear in the lowest lettered simulation channel. The WRITE and CLEAR buttons apply to experimentally assigned frequencies and are explained below. SCALING section: Enter -1 in the associated channel (CHN) field. If set to a value between 0 and 8, the simulation will scale and offset with the experiment data in this channel. Use the SCALAR and OFFSET factors accordingly. Lorentzian and/or Gaussian line shapes will be convoluted with each calculated line upon entering non-zero value(s) for the full widths in the edit fields. The WIDTHS field corresponds to the number of full widths to extend the lineshape function. DIALOGS section: Access to the quantum numbers is provided by checking the JKK(M) QN box. To retrieve the quantum numbers for a simulated line shown on the display, move the mouse cursor and click near a line so that the horizontal cross hair extends over the line of interest. Depress the CALL button from the JKK QN DIALOG or use the hot key, j, from the MAIN WINDOW display. The band type, quantum numbers and simulated intensities and frequencies are displayed in a sequential list for all lines under the horizontal cross hair. If more than five lines are found, the list may be scrolled using the up/down scroll list controls or the hot key, spacebar, from the MAIN WINDOW display. Select a line from the displayed list by clicking its associated radio button. Reposition the cursor cross at the desired experimental frequency and depress the ASSIGN button or use the hot key, k, from the MAIN WINDOW display. The experimental frequency field is filled in and a vertical line is displayed showing the location of this frequency. The lower-case band-type letter above the simulated line changes to an upper-case letter indicating the simulated line has been assigned. To remove (zero) experimental assigned lines, select the line from the list as above and depress the CLEAR button or use the hotkey, K, from the MAIN WINDOW display. The experimental assigned frequencies exist in random access memory (RAM) memory only. To save the assignments to disk for use by the rotor program, depress the WRITE button in the SIMULATIONS section. Upon entering a filename and selecting SAVE from the SAVE AS dialog, all assigned lines for that simulation are written to an ASCII assignment file. This newfile name will also appear in the LINEAR LEAST SQUARE section of ROTORCALCULATION OPTIONS dialog. The file can be viewed or edited using WORDPAD but must always be terminated with // for the rotor program to read it properly. The assigned lines in this file are used by the rotor program to refine the parameters if LSF CYCS is greater than 0.However, regardless of the value of LSF CYCS, transitions in the assignment file will always appear in the new simulated line set when the rotor program is run and the generic files renamed. The original assignments from a simulated line set on disk will be restored in RAM memory upon using either the OPEN, RD IAR buttons or by modifying the simulation file name field. If new assignments have been made, first save them using the WRITE button or all new information stored in RAM memory will be lost. To start from `scratch,' first clear all experimental assignments using the CLEAR button. Another feature that is useful when making assignments in congested spectra is quantum number filtering. The JKK FILTER check box activates this dialog. Scrolled lists are provided to select between the specific quantum numbers, J  Ka Kc
(for upper state) J Ka Kc
(for lower
state) and/or P, Q or R branch types. The filtered
simulation
line set is updated on the display when selection is made in either
scrolled
list or the numeric value is changed. Filtering is disabled when the
dialog is
unchecked.
The TM/DIPOLE TB (track bar) dialog is used to scale the hybrid band intensities for any or all of the different band types using three vertical track bars. The square of the dipole components are given in terms of a percentage along each of the principal axes. Notice that the track bars are operative only for TM/DIPOLE components that have been calculated and always scale relative to these values. These scale factors apply even after the dialog display status box is unchecked. The ABC RIGID TB actives a horizontal track bar dialog used to make small step-wise changes in the rotational constants. The initial values are the exact values used to generate the simulated line set. These initial values are restored in the track bar dialogs each time the simulated line set is reread. The relative changes per unit track bar step is adjustable in the percent field. The new transition frequencies are calculated based on the derivative approximation and therefore, the modified spectrum is only approximate. The CALC button control is used to generate an exact line set based on the track bar values using the rotor program. These values are automatically copied into the CALC/FIT parameter fields of the ROTORCALCULATION OPTIONS DIALOG. Other important parameters used in the calculation such as J MAX, TEMP and/or TM DIPOLE components should be set prior to using this option. Separate track bars are provided for A, B and C in each state and the band origin. By checking the box, B+C/B-C, the B and C track bars are redefined in terms of B+C (+) and B-C (-),respectively. For two-state problems, the DELTA check box redefines the upper state constants in terms of differences relative to the ground state. Similar track bar dialogs are available for the Coriolis coupling parameters and Watson's D centrifugal distortion parameters (A reduction in IRrepresentation). The COPY S->I control will copy all modified or unmodified values into the CALC/FIT parameter fields of the ROTOR CALCULATION OPTIONS DIALOG. An additional dialog is provided to view residuals (difference between simulated and the active experimental traces). If the simulated sum option is activated, the residuals are displayed only for the lowest lettered simulation. EXTRAS section: The WRITE SIM control is used to create binary files (4-byte floating precision) from simulated line sets. If the simulated sum option is activated, the binary file will be created using all summed simulations. If viewed from an experimental channel (ANALYSIS OPTIONS DIALOG), the binary file will be an exact duplicate of the simulation if the scalar is 1.0 and offset is -(SIM OFFSET). The READ ASCII control is used to read simulated line sets in ASCII form generated using other programs and is explained in more detail in Section F.
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