9. Relaxed Scans

Pysisyphus currently supports 1d-relaxed scans, where one internal coordinate is kept frozen, while the remaining ones are relaxed. A sample input is given below.

 type: redund
 fn: lib:h2o2_hf_321g_opt.xyz
 type: pyscf
 basis: 321g
 pal: 4
 type: BOND
 indices: [2, 3]
 # start is optional; if not specified the initial value of the primitive
 # internal coordinate is used.
 start: 3.0
 end: 5.0
 # steps is optional and can be omitted, but then step_size must be given
 steps: 5
 # step_size: 0.4
 # Enable symmetric scan in both directions, starting from the initial coordinates
 # symmetric: False
 # By specifying an 'opt' block, the default optimization values, e.g.
 # convergence thresholds can be altered.
 # opt:
  # thresh: gau

If no start value is specified in the scan: block, then the initial value is used. Specification of steps is mandatory, as it determines the number of optimizations to carry out. If not directly given (step_size), a suitable step size is derived from an end value. Either end or step_size must be given.

The values step_size, start, end have to be provided in atomic units or radians. When the appropriate YAML constructor is used, inputs can still be in Ångström or degrees. The constructor !angstrom converts input in Ångström to Bohr and !deg converts input from degrees to radians. See below for an example.

 indices: [0, 1, 2, 3]
 steps: 5
 step_size: !deg 10.

In the example above, a relaxed scan around a torsion is carried out. In total, 5 steps of 10 degree each will be taken. By using the YAML constructor !deg, the input can be given in degrees, instead of radians. Internally, the degrees input is then converted to the appropriate unit, in this case radians.

Naive relaxed scan around the equilibrium value of a primitive internal may be affected by hysteresis, if the system under study is sufficiently complicated.

Relaxed scans are always carried out in redundant internal coordinates. Please see Optimization of Minima for the available optimization options. Supported primitive internals (type) are found in: Types of Primitive Coordinates.

All geometries, including the initial one are written to relaxed_scan.trj in the current working directory.