amplitude file for diffraction analysis from quantum chemical calculation

1. perform quantum chemical calculation
	optimize the structure of interest
	calculate hessian or frequency
	generate fchk from chk, for Gaussian98
	take dat, and convert geometry to non-unique cartesian, for GAMESS

2. make zmx file, molecule.zmx
	at this time, it only requires:
		title
		number of atoms
		list of names of atoms with one atom per line

3. run amplitude.x to generate redundant coordinate
	amplitude.x molecule.dat  zmt=molecule.zmx task=build > molecule.rc
	amplitude.x molecule.fchk zmt=molecule.zmx task=build > molecule.rc

4. combine zmx and rc to make zmt
	cat molecule.zmx molecule.rc > molecule.zmt

5. edit and trim redudant coordinate to as minimal as possible
	zmt should be formatted as:
		title
		number of atoms
		list of names of atoms with one atom per line
		blank line
		list of redundant coordinates with one coordinate per line

	redundant coordinates should be formatted as:
		type    list_of_atomic_indices    anharmoinicity

	for examples:
		r  C2  C1  2.0
		a  C3  C2  C1  0.0
                d  C4  C3  C2  C1  0.0

6. run amplitude.x to generate amp file at temperature of TEMPERATURE
	amplitude.x molecule.dat  Tv=TEMPERATURE Tr=TEMPERATURE zmt=molecule.zmt task=METHOD 1> molecule.amp 2> molecule.log
	amplitude.x molecule.fchk Tv=TEMPERATURE Tr=TEMPERATURE zmt=molecule.zmt task=METHOD 1> molecule.amp 2> molecule.log

	TEMPERATURE is the vibrational and rotational temperatures of molecule in Kelvin
	METHOD should be shrunk or jump or walk

7. investigate and make sure that the output makes sense
	program is flexible, but not fool-proof, and it is YOUR responsibility to make sure.


