alpha=0.995 temp=0.1 gamma=2.99 seed=25062025
Initialization ...
Here is the filename: graph.txt
grab
N = 1458
gamma = 2.99
avg_kp = 2.0101
T = 0.1
idum = 25062025
q = 1
num avg = 20
grid size multiplier coefficient = 1
A. Extract GCC of the network
Saving temporary largest connected component to: /tmp/1758436580_graph.txt_tmp_gcc.net
save temp 
 ctr = 1458
grab
num_nodes
grab
B. Infer all model parameters except gamma, T and q
inferred N = 1805.19
inferred kp_max = 51.0948
inferred avg_k = 2.24885
inferred mu = 0.273734
inferred Rh = 15.2986
C. Infer radial coordinates
D. Infer angular core coordinates
total nodes for the core = 736
initializing angles
Replica 1
**********************
size = 85
iter = 0
best_iter = 0
L = -724.084
Lmax = -724.084
Replica 2
**********************
size = 85
iter = 1
best_iter = 0
L = -912.283
Lmax = -724.084
Replica 3
**********************
size = 85
iter = 2
best_iter = 0
L = -814.751
Lmax = -724.084
Replica 4
**********************
size = 85
iter = 3
best_iter = 3
L = -697.464
Lmax = -697.464
Replica 5
**********************
size = 85
iter = 4
best_iter = 3
L = -823.389
Lmax = -697.464
Replica 6
**********************
size = 85
iter = 5
best_iter = 3
L = -809.041
Lmax = -697.464
Replica 7
**********************
size = 85
iter = 6
best_iter = 3
L = -872.352
Lmax = -697.464
Replica 8
**********************
size = 85
iter = 7
best_iter = 3
L = -826.57
Lmax = -697.464
Replica 9
**********************
size = 85
iter = 8
best_iter = 3
L = -800.625
Lmax = -697.464
Replica 10
**********************
size = 85
iter = 9
best_iter = 3
L = -932.35
Lmax = -697.464
Replica 11
**********************
size = 85
iter = 10
best_iter = 3
L = -720.863
Lmax = -697.464
Replica 12
**********************
size = 85
iter = 11
best_iter = 3
L = -837.143
Lmax = -697.464
Replica 13
**********************
size = 85
iter = 12
best_iter = 3
L = -783.9
Lmax = -697.464
Replica 14
**********************
size = 85
iter = 13
best_iter = 3
L = -879.537
Lmax = -697.464
Replica 15
**********************
size = 85
iter = 14
best_iter = 3
L = -711.676
Lmax = -697.464
Replica 16
**********************
size = 85
iter = 15
best_iter = 3
L = -852.207
Lmax = -697.464
Replica 17
**********************
size = 85
iter = 16
best_iter = 3
L = -998.48
Lmax = -697.464
Replica 18
**********************
size = 85
iter = 17
best_iter = 3
L = -723.252
Lmax = -697.464
Replica 19
**********************
size = 85
iter = 18
best_iter = 3
L = -741.639
Lmax = -697.464
Replica 20
**********************
size = 85
iter = 19
best_iter = 3
L = -717.712
Lmax = -697.464
Loptimal = -697.464
resuming the rest of the calculations
iter = 10
noise = 0.397699;    iter= 10/20; L = -1040.47
i = 10
mult = 1.19755
min = 101.312
max = 121.326
iter = 11
noise = 0.358929;    iter= 11/20; L = -1363.87
i = 11
mult = 1.19755
min = 121.326
max = 145.294
iter = 12
noise = 0.320159;    iter= 12/20; L = -1793.06
i = 12
mult = 1.19755
min = 145.294
max = 173.996
iter = 13
noise = 0.281389;    iter= 13/20; L = -2686.69
i = 13
mult = 1.19755
min = 173.996
max = 208.368
iter = 14
noise = 0.242619;    iter= 14/20; L = -3522.18
i = 14
mult = 1.19755
min = 208.368
max = 249.53
iter = 15
noise = 0.20385;    iter= 15/20; L = -4190.57
i = 15
mult = 1.19755
min = 249.53
max = 298.824
iter = 16
noise = 0.16508;    iter= 16/20; L = -5689.78
i = 16
mult = 1.19755
min = 298.824
max = 357.856
iter = 17
noise = 0.12631;    iter= 17/20; L = -7005.5
i = 17
mult = 1.19755
min = 357.856
max = 428.549
iter = 18
noise = 0.0875398;    iter= 18/20; L = -8148.87
i = 18
mult = 1.19755
min = 428.549
max = 513.208
iter = 19
noise = 0.0487699;    iter= 19/20; L = -10652.7
i = 19
mult = 1.19755
min = 513.208
max = 614.59
iter = 20
noise = 0.01;    iter= 20/20; L = -12954.3
i = 20
mult = 1.19755
min = 614.59
max = 736
iter = 21
noise = -0.0287699;    iter= 21/20; L = -15688
i = 21
mult = 1.19755
min = 736
max = 881.394
Control sum = 736
E. Infer remaining node coordinates
embed remaining nodes
embed list compiled
embed list size = 722
remaining num to embed = 700
remaining num to embed = 600
remaining num to embed = 500
remaining num to embed = 400
remaining num to embed = 300
remaining num to embed = 200
remaining num to embed = 100
remaining num to embed = 0
output resulting angles
output filename = results/yeast//kvk-coordinates.txt
E2. Massage All
error value = 0.0001
core size = 1458
start core massaging...
max_error = 1.26401
iter = 0; L = -17146.1
max_error = 1.08259
iter = 1; L = -16960.8
max_error = 0.831956
iter = 2; L = -16554.3
max_error = 1.04778
iter = 3; L = -16629.5
max_error = 1.04778
iter = 4; L = -16538.2
max_error = 1.06518
iter = 5; L = -16256.7
max_error = 1.06518
iter = 6; L = -16480.8
max_error = 1.07563
iter = 7; L = -16427.9
max_error = 1.09303
iter = 8; L = -16239
max_error = 0.974677
iter = 9; L = -15813.3
max_error = 0.971196
iter = 10; L = -15950.7
max_error = 0.918981
iter = 11; L = -15955.1
max_error = 0.81107
iter = 12; L = -15791.4
max_error = 0.978158
iter = 13; L = -15672.8
max_error = 0.981639
iter = 14; L = -15649.6
max_error = 2.69429
iter = 15; L = -15838
max_error = 2.68732
iter = 16; L = -16011.8
max_error = 2.67688
iter = 17; L = -16203.6
max_error = 2.68384
iter = 18; L = -15544.8
max_error = 0.974677
iter = 19; L = -15849.1
Add small noise to angular coordinates
output coordinates
