simple commands manual 2006/08/17

{} is for optional arguments

---main menu--------------------------------------------------------------------

quit			:	quit program

load	olddata	name	: load data files, name.xl0 and name.snr
	dat	name	: load data file, name.dat, which has pixel, data, stdev
	mls	name	: for current molecule, load mls input, name.mls
	xyz	name	: for current molecule, load cartesian input, name.xyz
	zmx	name	: for current molecule, load zmatrix input, name.zmx
	ric	name	: load redundant coordiante input, name.ric
	amp	name	: load calculated amplitude, name.amp

add	mls	name	: for next molecule, add mls input, name.mls
	xyz	name	: for next molecule, add cartesian input, name.xyz
	zmx	name	: for next molecule, add zmatrix input, name.zmx

remove	molecule	: remove the last molecule
	ric		: remove redundant coordinate
	amp		: remove amplitude and use empirical
	atomicbackground: remove the additional atomic background

save	sms	name	: save the modified molecular scattering, sM(s) to the file, name
	smt	name	: save smt to the file, name
	raw	name	: save raw to the file, name
	frd	name	: save the radial distribution, f(r) to the file, name
	rfd	name	: save the scaled radial distribution, rf(r) to the file, name
	zmx	name	: save zmx to the file, name.zmx
	mls	name	: save mls to the file, name.mls
	molden		: print molden input format to the screen
	amplitudes	: print bond lengthes (re,rg,ra) and amplitudes (lh,lm) to the screen
	internal	: print redundant internal coordinate values to the screen

fit	all		: fit linear+nonlinear parameters
	cartesian	: evaluate the redundant error bar from cartesian differentiation
	difference	: evaluate the minimal error bar of fractions for difference data
	linear		: fit linear parameters only
	length		: fit camera length as well as other parameters marked to be fitted
	camera		: old module of fitting camera length by parabola approximation

set	range	I1 I2	: set data range from pixel I1 to I2-1
	background n {name}	: set the order of polynomial background to be <n>,
				 P=a0/s^0+a1/s^1+...+a(n-1)/s^(n-1)
				 if name is specified, type is changed accordingly 
				 {polynomial, polynomialxe, reciprocal, reciprocalxe}
	atomicbackground f	: set the coefficient of additional atomicbackground to be <f>
	molecule n	: change the current molecule to <n>th index
	reacant	n	: in difference mode, mark the first <n> molecules as reactants.
				for presentation purpose, it changes sM(s) and f(r) and R, but not X2
	temperature f	: change the temperature of the current molecule to <f> K
	voltage f	: change the acceleration voltage to <f> kV, scattering factors are interpolated accordingly from ITC values
	pixel f		: change the effective pixel size to <f> um
	camera	f	: change the camera distance to <f> cm
	cameravariance f: change the parameter for the uncertainty of camera distance to <f>
	noise	f	: set the noise rejector coefficient to <f>
	scalefactor f	: change the scalefactor to 1/<f>
	inversescalefactor f	: change the scalefactor to <f>
	fraction f	: change the fraction of the current molecule to <f>
	fifj S1 S2	: change the leveling atoms to those by symbols S1 and S2
	reference S0	: change the reference atom to one by symbol S0
	damping	f	: change the damping parameter k for f(r) sine transformation
	difference	: use the difference mode. it sets the fraction sum to be zero.
	fractionsum f	: change the sum of fractions to <f>
	echo y/n	: enable/disable the echo of input (useful for batch run)
	update y/n	: enable/disable the automatic update of fitted values
	method	name	: change the method of nonlinear fitting to marquardt, jacobieigen, monte carlo, or search
	detail	n	: change the degree of the detailed output to <n>
	coupled n1 n2	: set the fractions of <n1>th and <n2>th molecules to be same all the time
	profile	f	: change the electron width to <n> X 2 pixels
	limit	f	: change the limit value for distance in f(r) sine transformation
	jacobi	m {fl {fn {n}}}	: change the method of solving the alpha matrix to <m>:	1=GaussJordan, 2=CholeskyDecompose, 3=Jacobi-Eigen
					change the skipping criteria for linear parameters to <fl> when given
					change the skipping criteria for nonlinear parameters to <fn> when given
					change the number of nonlinear parameters to be inverse when <n> > 0

set	coordinate	: enter the structural parameters menu
set	structure	: enter the redundant structural parameters menu

set	fit	linear		: enable fitting linear parameters marked to be fitted
		background	: mark polynomial backgrounds to be fitted
		atomicbackground: mark the additional atomicbackground to be fitted
		scalefactor	: mark the scalefactor to be fitted
		d2yda2		: use d2yda2 term in evaluating alpha matrix
		camera		: mark the camera distance to be fitted
		cameravariance	: mark the parameter for the uncertainty of camera distance to be fitted
		temperature	: mark the temperature of the current molecule to be fitted
		temperatures	: mark the temperatures of all the molecules to be fitted
		fraction	: mark the fraction of the current molecule to be fitted
		fractions	: mark the fractions of all the molecules to be fitted
		fractionsum	: mark the sum of fractions to be fitted
		coordinates	: enable fitting the structural parameters
		structures	: enable fitting the redundant coordinates
		internal j1 j2	: enable fitting the redundant coordinate from #j1 to #j2

set	fix	linear		: disable fitting linear parameters marked to be fitted
		background	: mark polynomial backgrounds not to be fitted
		atomicbackground: mark the additional atomicbackground not to be fitted
		scalefactor	: mark the scalefactor not to be fitted
		d2yda2		: use only dyda term in evaluating alpha matrix
		camera		: mark the camera distance not to be fitted
		cameravariance	: mark the parameter for the uncertainty of camera distance not to be fitted
		temperature	: mark the temperature of the current molecule not to be fitted
		temperatures	: mark the temperatures of all the molecules not to be fitted
		fraction	: mark the fraction of the current molecule not to be fitted
		fractions	: mark the fractions of all the molecules not to be fitted
		fractionsum	: mark the sum of fractions not to be fitted
		coordinates	: disable fitting the structural parameters
		structures	: disable fitting the redundant coordinates
		internal j1 j2	: disable fitting the redundant coordinate from #j1 to #j2


get	range		: show the pixel range
	background 	: show the order of polynomial background + additional atomicbackground
	atomicbackground: show the coefficient of additional atomicbackground
	voltage f	: show the acceleration voltage
	pixel f		: show the effective pixel size
	camera		: show the camera distance
	noise		: show the noise rejector coefficient
	profile		: show the electron width
	fifj 		: show the leveling atoms
	reference 	: show the reference atom
	damping		: show the damping parameter k for f(r) sine transformation
	temperatures	: show the temperatures of all the molecules
	fits		: show which parameters are set to be fitted
	difference	: show the sum of fractions
	fractions	: show the fractions of all the molecules
	results		: show the formatted results of fitting
	compact		: show the brief-formatted results of fitting
	amplitudes	: ?
	xyz2zmx		: update zmatrix values from cartesian coordinate
	ensemble	: show the ensemble distribution of the current molecule
	jacobi		: show the setting for jacobi method

---coordinate menu--------------------------------------------------------------

done	: exit the coordinate menu and return to main menu
go	: start nonlinear fitting
fit	name name ...	: mark the variables by <name>'s to be fitted
fit	temperature	: mark the temperature of the current molecule to be fitted
fix	name name ...	: mark the variables by <name>'s not to be fitted
fix	temperature	: mark the temperature of the current molecule not to be fitted
rfit	name name ...	: enable fitting the ensemble distribution of the variable by <name>
rfix	name name ...	: disable fitting the ensemble distribution of the variable by <name>
loosen	name n f1 f2 f3 f4	: enable ensemble representation of variable <name> with <n>-fold symmetry, potential barrier of <f1>, temperature of mode of <f2>, in the range between <f3> and <f4>
fasten	name		: disable ensemble representation of variable <name>
set temperature	f	: set the temperature of the current molecule to <f> K
set <name>	f	: set the value of the variable of <name> to <f>
set molecule	n	: change the molecule to <n>th index

---structure menu---------------------------------------------------------------

done	: exit the coordinate menu and return to main menu
go	: start nonlinear fitting
fit	n1 n2 ...	: mark the variables of <n>th indices to be fitted
fit	temperature	: mark the temperature of the current molecule to be fitted
fix	name name ...	: mark the variables by <n>th indices not to be fitted
fix	temperature	: mark the temperature of the current molecule not to be fitted
set	temperature f	: set the temperature of the current molecule to <f> K
set	n	f	: set the value of the variable of <n>th index to <f>
set molecule	n	: change the molecule to <n>th index


