8. Optimization of clusters¶
8.1. Theoretical backgrounds¶
Optimization of clusters using the genetic algorithm
| [ga1] | G L W Hart, V Blum, M J Walorski and A Zunger, Nat. Mater. 4, 391 (2005). |
| [ga2] | V Blum, G L W Hart, M J Walorski and A Zunger, Phys. Rev. B 72, 165113 (2005). |
8.2. gasa¶
- Searching for the set of clusters that minimizes the CV score using the genetic algorithm.
- An initial population can be generated using the simulated annealing.
- Multi-thread calculations using OPENMP are available only for the simulated annealing.
Input files
- GASA.in
- ENERGY
- CORRELATION
Output files
- gasa.out
8.3. wgasa¶
- Searching for the set of clusters that minimizes the weighted CV score using the genetic algorithm.
Input files
- GASA.in
- ENERGY
- CORRELATION
- WEIGHT
Output files
- wgasa.out
8.4. GASA.in¶
Example
The set of clusters is optimized using the genetic algorithm. The cluster set is composed of no.0-5 clusters and 5 clusters selected among no.6-52 clusters.
NLOOP = 0 # only performing genetic algorithm
BASECLUSTER = 0 1 2 3 4 5
NPOP = 25
NELITE = 1
NALLCLUSTER = 53
MININDEX = 6
MAXINDEX = 52
NCLUSTER = 5
MAXGENE = 300
PMATING = 0.9
PMUTATION = 0.03
The initial population is generated by simulated annealing and the set of clusters is optimized using the genetic algorithm. The cluster set is composed of no.0-5 clusters and 5 clusters selected among no.6-52 clusters.
NLOOP = 100
TEMPINIT = 1
TEMPFINAL = 0.001
TEMPMUL = 0.9
BASECLUSTER = 0 1 2 3 4 5
NPOP = 25
NELITE = 1
NALLCLUSTER = 53
MININDEX = 6
MAXINDEX = 52
NCLUSTER = 5
MAXGENE = 300
PMATING = 0.9
PMUTATION = 0.03
8.4.1. NALLCLUSTER tag¶
Number of all clusters included in CORRELATION file.
- Default : none
- Example : NALLCLUSTER = 53
8.4.3. MININDEX tag, MAXINDEX tag¶
Minimum and maximum cluster index for the optimization.
- Default : MININDEX = 0, MAXINDEX = NALLCLUSTER - 1
- Example : MININDEX = 5
- Example : MAXINDEX = 52
8.4.4. BASECLUSTER tag¶
Cluster indexes included for ECI evaluation.
- Default : empty
- Example : BASECLUSTER = 0 1 2 3 4 5
8.4.5. EXCLUSTER tag¶
Cluster indexes excluded for the optimization.
- Default : empty
- Example : EXCLUSTER = 15 23 34
8.4.6. NPOP tag¶
Number of cluster sets included in the population.
- Default : 30
- Example : NPOP = 25
8.4.7. NELITE tag¶
Number of elites (good cluster sets) kept for the next optimization step.
- Default : 1
- Example : NELITE = 5
8.4.10. NLOOP tag¶
Number of steps for simulated annealing at one temperature. If you perform only the genetic algorithm, set NLOOP = 0.
- Default : 0
- Example : NLOOP = 100
8.4.11. TEMPINIT tag, TEMPFINAL tag¶
Initial and final temperatures in the simulated annealing.
- Default : none
- Example : TEMPINIT = 1
- Example : TEMPFINAL = 0.001
8.4.12. TEMPMUL tag¶
Exponential base used in an automatic setting of temperatures in the simulated annealing. Set values ranged from 0 to 1.
- Default : none
- Example : TEMPMUL = 0.9