uw-cmg StructOpt_modular issues

uw-cmg / StructOpt_modular

A flexible and modular Structure Optimization suite for combining experimental data with energy simulations to create atomic structures.

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issues

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move the logic of checking the V(k) file into one fuction

#55 jjmaldonis closed 7 years ago
1
Make the .fitness functions automatically take their individual

#54 jjmaldonis opened 7 years ago
0
Decouple parameters from `logging`

#53 jjmaldonis closed 7 years ago
1
Print warning when the user and StructOpt disagree on the number of cores to use

#52 jjmaldonis closed 8 years ago
1
Cluster rotate

#51 zhongnanxu closed 8 years ago
0
Input cleanup

#50 zhongnanxu closed 8 years ago
0
Adaptation

#49 zhongnanxu closed 8 years ago
0
Parallelism

#48 jjmaldonis closed 8 years ago
0
fix individual.copy to contain all the other relevant values

#47 jjmaldonis closed 8 years ago
0
Have lammps.py always copy input files for keep_files = True

#46 zhongnanxu closed 7 years ago
2
Logging

#45 jjmaldonis closed 8 years ago
0
Figure out how population.replace and .allgather work -- can we reduce them?

#44 jjmaldonis closed 8 years ago
1
move output relaxation files into logging directory?

#43 jjmaldonis closed 8 years ago
0
see #37: wrote better logger initializers; ...

#42 jjmaldonis closed 8 years ago
0
added genealogy tracking and printing;

#41 jjmaldonis closed 8 years ago
0
initialized the fitness logger -- BE CAREFUL it needs to be deleted a…

#40 jjmaldonis closed 8 years ago
0
Mutations

#39 zhongnanxu closed 8 years ago
0
Moved sphere.py tools into structopt/tools

#38 zhongnanxu closed 8 years ago
0
Implement logging throughout postprocessing methods when desired

#37 jjmaldonis closed 8 years ago
0
bugfixes for master and start of logging implementation

#36 jjmaldonis closed 8 years ago
0
Generators

#35 zhongnanxu closed 8 years ago
0
delete one of the .generation variables so there is only one

#34 jjmaldonis closed 8 years ago
0
changed selection functions to not include a random probability of ac…

#33 jjmaldonis closed 8 years ago
0
More robust lammps error checking

#32 zhongnanxu closed 8 years ago
0
Parameters

#31 zhongnanxu closed 8 years ago
0
TXF: Genealogy Tree Issue

#30 cmgtam closed 8 years ago
1
TXF: StructOpt atoms too close for VASP

#29 cmgtam closed 8 years ago
1
TXF: syntax error reported

#28 cmgtam closed 8 years ago
1
TXF: occasionally structopt will fail on multiple cores on a single node

#27 cmgtam closed 7 years ago
3
TXF: Running VASP with ASE

#26 cmgtam closed 8 years ago
1
TXF: Submitting Mutations

#25 cmgtam closed 8 years ago
1
TXF: 1 percent of lammps runs with bad energies

#24 cmgtam closed 7 years ago
0
ENH: Add functionality for Defect structure type

#23 jjmaldonis closed 7 years ago
1
ENH: add genealogy tracking

#22 jjmaldonis closed 8 years ago
0
BUG: Add assertion statements throughout code to ensure things are working

#21 jjmaldonis closed 8 years ago
0
ENH: allow the population to be sorted by implementing <, >, ==, etc for individuals based on their total fitness values

#20 jjmaldonis closed 8 years ago
0
BUG: Running with LAMMPS keep_files=False causes hangup

#19 zhongnanxu closed 8 years ago
1
ENH: Implement crossover schemes analogous to selection schemes

#18 jjmaldonis closed 8 years ago
1
BUG: Figure out how to consistently name files/classes/functions and match them up with input parameter names

#17 jjmaldonis opened 8 years ago
0
CRITICAL: Get the entire code to run in parallel with mpi4py

#16 jjmaldonis closed 8 years ago
1
ENH: Add predators if necessary

#15 jjmaldonis closed 8 years ago
1
ENH: Add fingerprinters if necessary

#14 jjmaldonis closed 8 years ago
1
ENH: Only run crossover and mutate if generation > 1

#13 zhongnanxu closed 8 years ago
0
CRITICAL: Add multi-core functionality for LAMMPS

#12 zhongnanxu closed 8 years ago
1
ENH: Add generation functions

#11 zhongnanxu closed 8 years ago
2
BUG: Add assertions of probabilities > 1.0

#10 zhongnanxu closed 7 years ago
0
ENH: Update convergence criteria to maxgen

#9 zhongnanxu closed 8 years ago
2
TEST: perform tests on lammps.py and structopt_lammps.py

#8 zhongnanxu opened 8 years ago
0
TEST: test hard-sphere cutoff relaxation method

#7 jjmaldonis opened 8 years ago
2
ENH: add more selections, crossovers, mutations, and predators

#6 jjmaldonis closed 8 years ago
0