-----Global Cluster Optimization Run----
GAv14
Local time : 'Mon Jan  6 10:02:25 2014'

--------------------
General Algorithm Information

Algorithm Performed in serial
Algorithm type : Random
Type of structure to optimize (type) = 'Defect'
Random number seed = 10
Concentration in individual held constant through crossover
Structure Fingerprinting (fingerprinting) : False

--------------------
Population Generation Parameters

Number of clusters in population (nclust) : 5
Starting cluster configuration (atomlist) : [('Si', 0, 28.0855, -5.3062), ('C', 4, 12.011, -7.371)]
Number of atoms in Initial Individual (natoms) : 4
Starting cluster unit size (size) : 3.9684842915868095
Average distance between atoms (r_ab) : 2.5
File for bulk solid for Defect run (SolidFile) : 'cBulk.xyz'
Cell size for bulk solid for Defect run (SolidCell) : [13.092, 13.092, 13.092]
Size of bulk solid supercell (supercell) : (3, 3, 3)
Evaluation of energy of bulk solid (EvalSolid) : False
Scale factor for surrounding material to include in Defect run (sf) : 1.75
Start from random location option (Random_loc_start) : False
Start from random location option (random_vac_start) : False
Interstitial finding scheme is (FindInts) : False
Vacancy finding scheme is (TrackVacs) : False
Substitutions finding scheme is (TrackSwaps) : False
Allow free exchange between bulk and cluster (Alloy) : True

--------------------
Crossover Configuration Parameters

Crossover probability (CXPB) : 0.8
Crossover scheme (CX_SCHEME) : 'cxTP'
Parent selection scheme (SELECTION_SCHEME) : 'Tournament'
    Tournament Size (tournsize) : 3

--------------------
Mutation Configuration Parameters

Mutation Probability (MUTPB) : 0.1
Mutation Options (mutation_options) : ['Lattice_Alteration_small', 'Lattice_Alteration_Group', 'Rotation_geo']

--------------------
Individual Evaluation Parameters


----LAMMPS Input------
The potential used is 'SiC.tersoff'
The potential style is 'tersoff'
Lammps minimizer used '1e-25 1e-25 5000 10000''cg'

--------------------
Selection Parameters

Fitness Scheme (FIT_SCHEME) : 'totalenfit'
Natural Selection Scheme (NAT_SELECT): 'Tournament'
    Tournament Size (tournsize) = 3

--------------------
Convergence Parameters

Population convergence scheme (CONVERGENCE_SCHEME) : 'Max-Gen'
Maximum number of generation (maxgen) = 5
Duplicate structure convergence control scheme (predator) 'FITpred'
Minimum energy difference for duplicate consideration (demin) : 0.005

--------------------
Output and Post-Processing Parameters

Structure atoms filename (filename) : /home/tam/test_amy_GA/GA_test
Summary filename : '//home/tam/test_amy_GA/GA_test/Summary-GA_test.txt'
Format for summary file (output_format) : 'totalenergy'
Genealogy File name : '//home/tam/test_amy_GA/GA_test/Genealogy-GA_test.txt'
All Energy file written 
Vacancies output to final structures : False

-------- Generation 0 --------

----Initialize Structures----
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6


New atomlist concentrations based on cluster+box = [('Si', 1, 28.0855, -5.3062), ('C', 5, 12.011, -7.371)]

---Starting Structures---

--New Population--
Individual 0
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.90457297,  6.26924802,  6.58068964],
       [ 5.45486835,  7.79486115,  7.5549429 ],
       [ 7.23026623,  5.20307702,  6.35281157],
       [ 5.937732  ,  5.55931643,  8.06778233],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 0
     Energy = 0
     Fitness = 0
Individual 1
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 7.42325882,  5.37548006,  7.97557897],
       [ 5.86219051,  6.71305612,  5.68757784],
       [ 6.14702544,  7.011586  ,  7.28387393],
       [ 6.09496477,  5.72638043,  7.6091957 ],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 1
     Energy = 0
     Fitness = 0
Individual 2
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 7.43725904,  8.47549242,  7.92370547],
       [ 3.71421512,  4.64458351,  6.02139549],
       [ 7.27292022,  5.83038812,  6.94277069],
       [ 7.10304518,  5.87603856,  7.66835479],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 2
     Energy = 0
     Fitness = 0
Individual 3
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.62107357,  5.55554402,  7.63437551],
       [ 7.24036176,  5.91836167,  6.20473993],
       [ 5.5291605 ,  5.44415142,  7.28537618],
       [ 7.13684372,  7.90844551,  7.43173482],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 3
     Energy = 0
     Fitness = 0
Individual 4
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.98530756,  5.0195132 ,  8.12045829],
       [ 5.07666138,  6.81174584,  6.3174974 ],
       [ 6.66936446,  4.80885692,  6.52960513],
       [ 6.79610615,  8.18638664,  7.58866563],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 4
     Energy = 0
     Fitness = 0
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220

--Evaluate Structures--
----Individual 0 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
WARNING: Exception during energy eval:
RuntimeError('Please set LAMMPS_COMMAND environment variable',)
EnergypAtm = 0
----Individual 1 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0
----Individual 2 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0
----Individual 3 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0
----Individual 4 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0

----Stats----
  Min 10
  Max 10
  Avg 10
  Std 0.0
  Genrep 0

--New Population--
Individual 0
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.90457297,  6.26924802,  6.58068964],
       [ 5.45486835,  7.79486115,  7.5549429 ],
       [ 7.23026623,  5.20307702,  6.35281157],
       [ 5.98394142,  5.57122714,  8.10981157],
       [ 5.46799686,  5.43823976,  7.64054026],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 0
     Energy = 10
     Fitness = 10
Individual 1
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 7.42325882,  5.37548006,  7.97557897],
       [ 5.86219051,  6.71305612,  5.68757784],
       [ 6.14702544,  7.011586  ,  7.28387393],
       [ 6.11811571,  5.73713778,  7.60747881],
       [ 5.47568302,  5.43862422,  7.6551223 ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 1
     Energy = 10
     Fitness = 10
Individual 2
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 7.43725904,  8.47549242,  7.92370547],
       [ 3.71421512,  4.64458351,  6.02139549],
       [ 7.27292022,  5.83038812,  6.94277069],
       [ 7.10304518,  5.87603856,  7.66835479],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 2
     Energy = 10
     Fitness = 10
Individual 3
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.87227695,  5.79665367,  7.94570759],
       [ 7.24036176,  5.91836167,  6.20473993],
       [ 5.66517856,  5.53631897,  7.06453793],
       [ 7.13684372,  7.90844551,  7.43173482],
       [ 5.37387013,  5.35353137,  7.68568855],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 3
     Energy = 10
     Fitness = 10
Individual 4
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.98530756,  5.0195132 ,  8.12045829],
       [ 5.07666138,  6.81174584,  6.3174974 ],
       [ 6.69889025,  4.92891135,  6.52614717],
       [ 6.79610615,  8.18638664,  7.58866563],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 4
     Energy = 10
     Fitness = 10
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220
-----Global Cluster Optimization Run----
GAv14
Local time : 'Mon Jan  6 10:03:26 2014'

--------------------
General Algorithm Information

Algorithm Performed in serial
Algorithm type : Random
Type of structure to optimize (type) = 'Defect'
Random number seed = 5
Concentration in individual held constant through crossover
Structure Fingerprinting (fingerprinting) : False

--------------------
Population Generation Parameters

Number of clusters in population (nclust) : 5
Starting cluster configuration (atomlist) : [('Si', 0, 28.0855, -5.3062), ('C', 4, 12.011, -7.371)]
Number of atoms in Initial Individual (natoms) : 4
Starting cluster unit size (size) : 3.9684842915868095
Average distance between atoms (r_ab) : 2.5
File for bulk solid for Defect run (SolidFile) : 'cBulk.xyz'
Cell size for bulk solid for Defect run (SolidCell) : [13.092, 13.092, 13.092]
Size of bulk solid supercell (supercell) : (3, 3, 3)
Evaluation of energy of bulk solid (EvalSolid) : False
Scale factor for surrounding material to include in Defect run (sf) : 1.75
Start from random location option (Random_loc_start) : False
Start from random location option (random_vac_start) : False
Interstitial finding scheme is (FindInts) : False
Vacancy finding scheme is (TrackVacs) : False
Substitutions finding scheme is (TrackSwaps) : False
Allow free exchange between bulk and cluster (Alloy) : True

--------------------
Crossover Configuration Parameters

Crossover probability (CXPB) : 0.8
Crossover scheme (CX_SCHEME) : 'cxTP'
Parent selection scheme (SELECTION_SCHEME) : 'Tournament'
    Tournament Size (tournsize) : 3

--------------------
Mutation Configuration Parameters

Mutation Probability (MUTPB) : 0.1
Mutation Options (mutation_options) : ['Lattice_Alteration_small', 'Lattice_Alteration_Group', 'Rotation_geo']

--------------------
Individual Evaluation Parameters


----LAMMPS Input------
The potential used is 'SiC.tersoff'
The potential style is 'tersoff'
Lammps minimizer used '1e-25 1e-25 5000 10000''cg'

--------------------
Selection Parameters

Fitness Scheme (FIT_SCHEME) : 'totalenfit'
Natural Selection Scheme (NAT_SELECT): 'Tournament'
    Tournament Size (tournsize) = 3

--------------------
Convergence Parameters

Population convergence scheme (CONVERGENCE_SCHEME) : 'Max-Gen'
Maximum number of generation (maxgen) = 5
Duplicate structure convergence control scheme (predator) 'FITpred'
Minimum energy difference for duplicate consideration (demin) : 0.005

--------------------
Output and Post-Processing Parameters

Structure atoms filename (filename) : /home/tam/test_amy_GA/GA_test
Summary filename : '//home/tam/test_amy_GA/GA_test/Summary-GA_test.txt'
Format for summary file (output_format) : 'totalenergy'
Genealogy File name : '//home/tam/test_amy_GA/GA_test/Genealogy-GA_test.txt'
All Energy file written 
Vacancies output to final structures : False

-------- Generation 0 --------

----Initialize Structures----
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6


New atomlist concentrations based on cluster+box = [('Si', 1, 28.0855, -5.3062), ('C', 5, 12.011, -7.371)]

---Starting Structures---

--New Population--
Individual 0
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.62817877,  6.32462779,  7.54254533],
       [ 7.89630232,  6.31713364,  8.04706441],
       [ 4.27130997,  5.22867396,  8.13052846],
       [ 6.7316485 ,  6.95606722,  4.83608824],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 0
     Energy = 0
     Fitness = 0
Individual 1
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.77293355,  5.22751322,  7.64509779],
       [ 7.189117  ,  4.30103626,  6.34728017],
       [ 6.02056179,  7.88549502,  8.52596079],
       [ 5.54482722,  7.41245812,  6.03788769],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 1
     Energy = 0
     Fitness = 0
Individual 2
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.42650059,  4.9754134 ,  5.97104018],
       [ 6.434306  ,  5.30383385,  6.81913031],
       [ 6.8748727 ,  7.934746  ,  7.11209968],
       [ 6.79176026,  6.61250936,  8.65395627],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 2
     Energy = 0
     Fitness = 0
Individual 3
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.60943865,  7.65697885,  8.15531105],
       [ 8.63256966,  7.46953017,  6.6002484 ],
       [ 6.23015095,  4.58132437,  5.99272509],
       [ 5.0552803 ,  5.11866922,  7.8079419 ],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 3
     Energy = 0
     Fitness = 0
Individual 4
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.71455667,  5.96749146,  6.94600047],
       [ 6.93119399,  6.52539616,  7.5128918 ],
       [ 6.95435079,  5.18682765,  8.40153047],
       [ 5.9273381 ,  7.14678734,  5.69580371],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 4
     Energy = 0
     Fitness = 0
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220

--Evaluate Structures--
----Individual 0 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
WARNING: Exception during energy eval:
RuntimeError('Please set LAMMPS_COMMAND environment variable',)
EnergypAtm = 0
----Individual 1 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0
----Individual 2 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0
----Individual 3 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0
----Individual 4 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0

----Stats----
  Min 10
  Max 10
  Avg 10
  Std 0.0
  Genrep 0

--New Population--
Individual 0
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.62817877,  6.32462779,  7.54254533],
       [ 7.89630232,  6.31713364,  8.04706441],
       [ 4.27130997,  5.22867396,  8.13052846],
       [ 6.7316485 ,  6.95606722,  4.83608824],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 0
     Energy = 10
     Fitness = 10
Individual 1
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.77293355,  5.22751322,  7.64509779],
       [ 7.21177853,  4.29892387,  6.34025874],
       [ 6.02056179,  7.88549502,  8.52596079],
       [ 5.55066315,  7.39816565,  6.07611763],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 1
     Energy = 10
     Fitness = 10
Individual 2
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.42650059,  4.9754134 ,  5.97104018],
       [ 6.434306  ,  5.30383385,  6.81913031],
       [ 6.8748727 ,  7.934746  ,  7.11209968],
       [ 7.07004982,  6.71737311,  8.51778677],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.46596681,  6.48974542,  8.81336983]])
 	Genealogy = 2
     Energy = 10
     Fitness = 10
Individual 3
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.60943865,  7.65697885,  8.15531105],
       [ 8.63256966,  7.46953017,  6.6002484 ],
       [ 6.22235182,  4.58657989,  5.97968227],
       [ 4.96790037,  5.05263403,  7.83924944],
       [ 5.51252664,  5.46422173,  7.64411415],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 3
     Energy = 10
     Fitness = 10
Individual 4
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.71455667,  5.96749146,  6.94600047],
       [ 6.93119399,  6.52539616,  7.5128918 ],
       [ 6.95435079,  5.18682765,  8.40153047],
       [ 5.9273381 ,  7.14678734,  5.69580371],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 4
     Energy = 10
     Fitness = 10
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220
-----Global Cluster Optimization Run----
GAv14
Local time : 'Mon Jan  6 10:03:56 2014'

--------------------
General Algorithm Information

Algorithm Performed in serial
Algorithm type : Random
Type of structure to optimize (type) = 'Defect'
Random number seed = 0
Concentration in individual held constant through crossover
Structure Fingerprinting (fingerprinting) : False

--------------------
Population Generation Parameters

Number of clusters in population (nclust) : 5
Starting cluster configuration (atomlist) : [('Si', 0, 28.0855, -5.3062), ('C', 4, 12.011, -7.371)]
Number of atoms in Initial Individual (natoms) : 4
Starting cluster unit size (size) : 3.9684842915868095
Average distance between atoms (r_ab) : 2.5
File for bulk solid for Defect run (SolidFile) : 'cBulk.xyz'
Cell size for bulk solid for Defect run (SolidCell) : [13.092, 13.092, 13.092]
Size of bulk solid supercell (supercell) : (3, 3, 3)
Evaluation of energy of bulk solid (EvalSolid) : False
Scale factor for surrounding material to include in Defect run (sf) : 1.75
Start from random location option (Random_loc_start) : False
Start from random location option (random_vac_start) : False
Interstitial finding scheme is (FindInts) : False
Vacancy finding scheme is (TrackVacs) : False
Substitutions finding scheme is (TrackSwaps) : False
Allow free exchange between bulk and cluster (Alloy) : True

--------------------
Crossover Configuration Parameters

Crossover probability (CXPB) : 0.8
Crossover scheme (CX_SCHEME) : 'cxTP'
Parent selection scheme (SELECTION_SCHEME) : 'Tournament'
    Tournament Size (tournsize) : 3

--------------------
Mutation Configuration Parameters

Mutation Probability (MUTPB) : 0.1
Mutation Options (mutation_options) : ['Lattice_Alteration_small', 'Lattice_Alteration_Group', 'Rotation_geo']

--------------------
Individual Evaluation Parameters


----LAMMPS Input------
The potential used is 'SiC.tersoff'
The potential style is 'tersoff'
Lammps minimizer used '1e-25 1e-25 5000 10000''cg'

--------------------
Selection Parameters

Fitness Scheme (FIT_SCHEME) : 'totalenfit'
Natural Selection Scheme (NAT_SELECT): 'Tournament'
    Tournament Size (tournsize) = 3

--------------------
Convergence Parameters

Population convergence scheme (CONVERGENCE_SCHEME) : 'Max-Gen'
Maximum number of generation (maxgen) = 5
Duplicate structure convergence control scheme (predator) 'FITpred'
Minimum energy difference for duplicate consideration (demin) : 0.005

--------------------
Output and Post-Processing Parameters

Structure atoms filename (filename) : /home/tam/test_amy_GA/GA_test
Summary filename : '//home/tam/test_amy_GA/GA_test/Summary-GA_test.txt'
Format for summary file (output_format) : 'totalenergy'
Genealogy File name : '//home/tam/test_amy_GA/GA_test/Genealogy-GA_test.txt'
All Energy file written 
Vacancies output to final structures : False

-------- Generation 0 --------

----Initialize Structures----
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6
Generated cluster individual with natoms = 6


New atomlist concentrations based on cluster+box = [('Si', 1, 28.0855, -5.3062), ('C', 5, 12.011, -7.371)]

---Starting Structures---

--New Population--
Individual 0
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 7.28188055,  6.75344596,  7.01553436],
       [ 4.95831276,  5.77450152,  6.95347741],
       [ 7.04129809,  4.9492076 ,  7.23787017],
       [ 6.24594816,  7.34934754,  7.34934451],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 0
     Energy = 0
     Fitness = 0
Individual 1
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.44426401,  5.7667808 ,  7.01820636],
       [ 5.31992543,  6.37769741,  8.46438743],
       [ 7.54112933,  6.34761509,  5.79503446],
       [ 7.22212078,  6.33440931,  7.2785982 ],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 1
     Energy = 0
     Fitness = 0
Individual 2
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.90911774,  4.19766316,  7.19994817],
       [ 6.45972215,  7.42130202,  9.31290625],
       [ 5.92843259,  7.23200086,  6.5107037 ],
       [ 7.23016707,  5.97553657,  5.53266833],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 2
     Energy = 0
     Fitness = 0
Individual 3
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.13669372,  6.96098475,  8.21872439],
       [ 5.93211247,  5.38279505,  6.90409607],
       [ 6.72362497,  6.34621627,  6.23590846],
       [ 6.73500839,  6.13650654,  7.19749752],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 3
     Energy = 0
     Fitness = 0
Individual 4
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.59676504,  7.38008632,  8.56075127],
       [ 6.42758169,  3.859666  ,  6.64347784],
       [ 6.66557594,  7.24235441,  5.80614051],
       [ 6.83751688,  6.34439589,  7.54585682],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 4
     Energy = 0
     Fitness = 0
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220

--Evaluate Structures--
----Individual 0 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
WARNING: Exception during energy eval:
RuntimeError('Please set LAMMPS_COMMAND environment variable',)
EnergypAtm = 0
----Individual 1 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0
----Individual 2 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0
----Individual 3 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0
----Individual 4 Optimization----
Defect configuration contains 108 'Si' atoms
Defect configuration contains 112 'C' atoms
--- WARNING: Atoms too close (<0.7A) - Implement Move ---
WARNING: Exception during energy eval:
OSError(2, 'No such file or directory')
EnergypAtm = 0

----Stats----
  Min 10
  Max 10
  Avg 10
  Std 0.0
  Genrep 0

--New Population--
Individual 0
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 7.28188055,  6.75344596,  7.01553436],
       [ 4.95831276,  5.77450152,  6.95347741],
       [ 7.04129809,  4.9492076 ,  7.23787017],
       [ 6.24594816,  7.34934754,  7.34934451],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 0
     Energy = 10
     Fitness = 10
Individual 1
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.44426401,  5.7667808 ,  7.01820636],
       [ 5.31992543,  6.37769741,  8.46438743],
       [ 7.54112933,  6.34761509,  5.79503446],
       [ 7.22212078,  6.33440931,  7.2785982 ],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 1
     Energy = 10
     Fitness = 10
Individual 2
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.90911774,  4.19766316,  7.19994817],
       [ 6.45972215,  7.42130202,  9.31290625],
       [ 5.92843259,  7.23200086,  6.5107037 ],
       [ 7.22340703,  5.98387206,  5.53384581],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 2
     Energy = 10
     Fitness = 10
Individual 3
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 6.13669372,  6.96098475,  8.21872439],
       [ 5.93211247,  5.38279505,  6.90409607],
       [ 6.72362497,  6.34621627,  6.23590846],
       [ 6.73500839,  6.13650654,  7.19749752],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 3
     Energy = 10
     Fitness = 10
Individual 4
Atoms(symbols='C5Si', positions=..., cell=[13.092, 13.092, 13.092], pbc=[True, True, True])
array([[ 5.59676504,  7.38008632,  8.56075127],
       [ 6.40474999,  3.77272679,  6.66102475],
       [ 6.66557594,  7.24235441,  5.80614051],
       [ 6.83751688,  6.34439589,  7.54585682],
       [ 5.4834    ,  5.44221   ,  7.65455   ],
       [ 6.55873   ,  6.5247    ,  8.76798   ]])
 	Genealogy = 4
     Energy = 10
     Fitness = 10
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220
Number of positions = 220
