How to generate the force filed parameters by vasprun.xml?

[harrypotty18]

Hi, When I went to calculate the force parameters in QuickFF 2.2.1 gave me an error with vasprun.xml file (version 5.3.5). The error reads:
" INIT Initializing system Traceback (most recent call last): File "/home/test/.conda/envs/quickff/bin/qff.py", line 38, in qff()
File "/home/test/.conda/envs/quickff/lib/python2.7/site-packages/quickff/scripts.py", line 360, in qff numbers, coords, energy, grad, hess, masses, rvecs, pbc = read_abinitio(fn)
File "/home/test/.conda/envs/quickff/lib/python2.7/site-packages/quickff/io.py", line 144, in read_abinitio vasprun = VASPRun(fn,field_labels=['hessian','gradient'])
File "/home/test/.conda/envs/quickff/lib/python2.7/site-packages/quickff/io.py", line 105, in init
self.fields['hessian'] = m3.reshape((-1,1))*self.fields['hessian']*m3 ValueError: operands could not be broadcast together with shapes (6,1) (2,2)".
Any suggestions on how to fix this issue would be appreciated. Thanks.

[camilofs]

Hello. I might be able to help. When you run the VASP calculations, set all of the atoms to update positions (T T T). The expected shape of the Hessian matrix should have the same form as the gradients (forces). For example, for three atoms:

• grad.shape = [9] --> [3, 3], i.e. three atoms and three directions
• hess.shape = [9, 9] --> [[3,3], [3,3]]

In case you want to study/model an isolated vibrational mode, you will have to use qff as a library and perform adjustments in the matrices by hand.