pele.systems.spawn_OPTIM

class pele.systems.spawn_OPTIM.PathInfoReader

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class PathInfoReader:

read path.info files

PathInfoReader.read_minimum()

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def read_minimum(self, fin):

the minima and transition states are stored as

1 line with energy 1 line with point group info natoms lines with eigenvalues natoms lines with coords

class pele.systems.spawn_OPTIM.SpawnOPTIM

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class SpawnOPTIM:

this class will control spawning of optim jobs and importing the results

1. make temp directory

2. make imput files (odata, finish, perm.allow, etc)

3. call OPTIM

4. when OPTIM finishes, load the results into the database

SpawnOPTIM.write_odata()

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def write_odata(self, fout):

write the odata file to the open file fout

stop after the line POINTS. i.e. don’t write coordinates

SpawnOPTIM.write_odata_coords()

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def write_odata_coords(self, coords, fout):

write the coords to odata

need to label the atoms correctly for the system

SpawnOPTIM.make_permallow_from_permlist()

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def make_permallow_from_permlist(self, permlist):

return a string corresponding to the perm.allow file from a permlist

SpawnOPTIM.write_perm_allow()

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def write_perm_allow(self, fname):

make the perm.allow file if appropriate

SpawnOPTIM.write_additional_input_files()

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def write_additional_input_files(self, rundir, coords1, coords2):

use this function to write any other input files that are needed

SpawnOPTIM.load_results()

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def load_results(self, database):

load the resulting min-ts-min triplets from the path.info file and put them in the database

Returns:

newminimaa set of the minima found

newtsa set of the transition states found