
run ueda.x
general instruction of experiment
	1. to set acceleration voltage of 60 kV, do "set voltage 60"
	2. to set pixel size of 60 um, do "set pixel 60"
	3. to set camera length of 25 cm, do "set camera 25"
	4. to set electron size of 10 pixel, do "set profile 10"
	5. to set pixel range of 50 to 500, do "set range 50 500"
	6. to set leveling function nuclear pair of carbon and oxygen, do "set fifj C O"
	7. to set scale factor, do "set scalefactor 2.3456789012345"

duing the fitting
	1. linear parameters are always fitted (fraction, scale factor, backgrounds)
	2. after every fitting, sM(s) is saved in _currentsms.dat
	3. use gnuplot to plot _currentsms.dat
	4. to save sM(s), do "save sms molecule_refined.sms"
	5. to see f(r), set two nuclear references, and damping k value, and do "save frd"
	6. to save f(r) as molecule.frd, do "save frd molecule_refined.frd"
	7. to save zmx, do "save zmx molecule_refined"

general instruction of molecules
	ueda.x can use 8 molecules at once.
	to load or replace with molecule.zmx
		load zmx molecule
	to add more
		add zmx molecule
	molecule specific commands (setting temperature, flaggin z-matrix or temperature) only applies to the current molecule
	the current molecule is shown in prompt as "#/#>"
		1/3> means the current molecule is the first one out of 3
	to change the current molecule to the second
		set molecule 2

examples:

to fit camera length
	1. load the data, which is "CO2.dat"
		load dat CO2
	1. or load the data of old format, which are "CO2.xl0" and "CO2.snr"
		load olddata CO2

	2. load bond lengths file, which is "CO2.mls"
		load mls CO2

	3. set data range, from pixel 34 to pixel 200
		set range 34 200

	4. set polynomial background, for example to use polynomial of 5th order, multiplied by Xe
		set background 5 polynomialxe

	5. fit camera length, accept the result
		set fit camera
		fit all
		yes

	6. to see summary
		get results

to fit a ground state
	0. set camera length of CO2 fitting
		set camera 26.67890123456789

	1. load the data, which is "GS.dat"
		load dat GS
	1. or load the data of old format, which are "GS.xl0" and "GS.snr"
		load olddata GS

	2. set data range, from pixel 34 to pixel 200
		set range 34 200

	3. set polynomial background, for example to use reciprocal of 5th order
		set background 5 reciprocal

	4. load z-mtrix structure, which is "gs.zmx"
		load zmx gs

	5. set temperature of molecule at 500 K
		set temperature 500

	6. if you wish to use amplitude, load "gs500K.amp", whose temperature is 500K
		load amp gs500K

	7. fit linear parameters
		fit linear

	8. if you wish to fit temperature
		set fit temperature

	9. to fit z-matrix, enter the structural parameters menu, flag those of interest (e.g. r1, r2, and a1)
		set coordinate
		fit r1
		fit r2
		fit a1
		done

	10. to fix z-matrix, enter the structural parameters menu, unflag those (e.g. t1)
		set coordinate
		fix t1
		done

	11. to fit z-matrix, enable z-matrix coordinate (nonlinear parameter) fitting
		set fit coordinates

	12. fit z-matrix and/or temperature, accept the result if acceptable
		fit all
		yes

	13. repeat until an agreement is achieved


to fit ground states
	0. set camera length of CO2 fitting
		set camera 26.67890123456789

	1. load the data, which is "GS.dat"
		load dat GS
	1. or load the data of old format, which are "GS.xl0" and "GS.snr"
		load olddata GS

	2. set data range, from pixel 34 to pixel 200
		set range 34 200

	3. set polynomial background, for example to use reciprocal of 5th order
		set background 5 reciprocal

	4. load z-mtrix structure, which is "trans.zmx"
		load zmx trans

	5. set temperature of trans at 500 K
		set temperature 500

	6. add second structure, which is "cis.zmx"
		add zmx cis

	7. set the current molecule to the second
		set molecule 2

	8. set temperature of cis at 500 K
		set temperature 500

	9. fit linear parameters
		fit linear

	10. if you wish to fix the fraction of trans as 12%
		set molecule 1
		set fraction 0.12
		set fix fraction

	11. to fit z-matrix of trans, enter the structural parameters menu, flag those of interest (e.g. r1, r2, and a1)
		set molecule 1
		set coordinate
		fit r1
		fit r2
		fit a1
		done

	12. to fix z-matrix of cis, enter the structural parameters menu, unflag those (e.g. t1)
		set molecule 2
		set coordinate
		fix t1
		done

	13. to fit z-matrix, enable z-matrix coordinate (nonlinear parameter) fitting
		set fit coordinates

	14. fit z-matrix and/or temperature, accept the result if acceptable
		fit all
		yes

	15. repeat until an agreement is achieved


to fit time-resolved
	0. set camera length of CO2 fitting
		set camera 26.67890123456789

	1. enable difference mode
		set difference yes

	2. load the data of time delay, which is "TR+0100.dat"
		load dat TR+0100
	2. or load the data of old format, which are "TR+0100.xl0" and "TR+0100.snr"
		load olddata TR+0100

	3. set data range, from pixel 34 to pixel 200
		set range 34 200

	4. set polynomial background, for example to use reciprocal of 5th order
		set background 5 reciprocal

	5. load refined GS z-mtrix structure, which is "GSrefined.zmx"
		load zmx GSrefined

	6. set temperature of GS at 500 K
		set temperature 500

	7. load amplitude for GS
		load amp GS500K

	8. add product (P1) structure, which is "P1.zmx"
		add zmx P1

	9. set temperature of P1 at 1500 K
		set molecule 2
		set temperature 1500

	10. load amplitude for P1
		load amp P11500K

	11. fit linear parameters
		fit linear

	12. to fit z-matrix of P1, enter the structural parameters menu, flag those of interest (e.g. r1, r2, and a1)
		set molecule 2
		set coordinate
		fit r1
		fit r2
		fit a1
		done

	13. to fix z-matrix of P1, enter the structural parameters menu, unflag those (e.g. t1)
		set molecule 2
		set coordinate
		fix t1
		done

	14. to fit z-matrix, enable z-matrix coordinate (nonlinear parameter) fitting
		set fit coordinates

	15. fit z-matrix and/or temperature, accept the result if acceptable
		fit all
		yes

	16. repeat until an agreement is achieved


to fit structure using redundant coordinate
	0. set camera length of CO2 fitting
		set camera 26.67890123456789

	1. load the data, which is "GS.dat"
		load dat GS
	1. or load the data of old format, which are "GS.xl0" and "GS.snr"
		load olddata GS

	2. set data range, from pixel 34 to pixel 200
		set range 34 200

	3. set polynomial background, for example to use reciprocal of 5th order
		set background 5 reciprocal

	4. load z-mtrix structure, which is "gs.zmx"
		load zmx gs

	5. set temperature of molecule at 500 K
		set temperature 500

	6. if you wish to use amplitude, load "gs500K.amp", whose temperature is 500K
		load amp gs500K

	7. load redundant coordinate, which is "GS.ric"
		load ric GS

	9. to fit redundant coordinates, enter the redundant parameters menu, flag those of interest (e.g. #1, #2, and #5)
		set structure
		fit 1
		fit 2
		fit 5
		done

	10. to fix redundant coordinates, enter the redundant parameters menu, unflag those (e.g. #13)
		set structure
		fix 13
		done

	11. to fit redundant coordinates, enable redundant coordinate (nonlinear parameter) fitting, choose eigenvalue method, set jacobi parameters of method 3, linear parameter eigenvalue threashold of 10^-15, nonlinear parameter eigenvalue threshold of 10^-15, the number of coordinate fitted of 4 of the largest eigenvalues
		set fit structures
		set method jacobieigen
		set jacobi 3 15 15 4

	12. fit redundant coordinates, accept the result if acceptable
		fit all
		yes

	13. repeat until an agreement is achieved

