

............................................................

+-------------------------------------------------+
|                                                 |
|                      PIMMS                      |
|                                                 |
| Polymer Interactions in Multicomponent Mixtures |
|                                                 |
+-------------------------------------------------+
         Version [0.1.4.post28+ge67335c.d20260704]


STARTING PIMMS...
............................................................

****************************************
  [STARTUP]: Parsing keyfile [KEYFILE.kf]
  [STARTUP]: Default values set are explicitly announced below:

No LATTICE_TO_ANGSTROMS set - using default [3.65]
No RESIZED_EQUILIBRATION set - using default [False]
No EQUILIBRATION_OFFSET set - using default [False]
No HARDWALL set - using default [False]
No REDUCED_PRINTING set - using default [False]
No ANGLES_OFF set - using default [False]
No CRANKSHAFT_MODE set - using default [UNIFORM]
No SLITHER_SUBSTEPS set - using default [10]
No PULL_SUBSTEPS set - using default [10]
No VMMC_MAX_DISPLACEMENT set - using default [3]
No VMMC_MAX_CLUSTER set - using default [1000]
No MOVE_VMMC set - using default [0.0]
No TSMMC_STEP_MULTIPLIER set - using default [50]
No TSMMC_INTERPOLATION_MODE set - using default [LINEAR]
No TSMMC_FIXED_OFFSET set - using default [False]
No ANA_INTSCAL set - using default [200]
No ANA_DISTMAP set - using default [200]
No ANA_ACCEPTANCE set - using default [200]
No ANA_INTER_RESIDUE set - using default [200]
No ANA_RESIDUE_PAIRS set - using default [[]]
No WRITE_CHAIN_TO_CHAINID set - using default [False]
No ANALYSIS_MODULE set - using default [False]
No ANA_CUSTOM set - using default [0]
No ANA_CLUSTER_THRESHOLD set - using default [1]
No RESTART_FILE set - using default [False]
No RESTART_OVERRIDE_DIMENSIONS set - using default [False]
No RESTART_OVERRIDE_HARDWALL set - using default [False]
No EXTRA_CHAIN set - using default [[]]
No CASE_INSENSITIVE_CHAINS set - using default [True]
No AUTOCENTER set - using default [False]
No SAVE_AT_END set - using default [False]
No SAVE_EQ set - using default [True]
No TRAJECTORY_PBC_UNWRAP set - using default [False]
No FREEZE_FILE set - using default [False]
No PARALLELIZE set - using default [False]
No PARALLEL_THREADS set - using default [0]
****************************************

KEYFILE SUMMARY
............................................................

--> System Overview
Total number of steps     : 100
Num. equilibration steps  : 10
Save equilibration frames : True
Expected number of frames : 3
Start temperature         : 100.00
Final temperature         : 90.00
Lattice-to-Angstroms      :  3.65
Autocenter                : False
Save at end only          : False

****************************************
--> Box Dimensions

BOX DIMENSIONS                 : 50 x 50 x 50
Total occupied volume fraction : 0.30720
Total conc. of solute(s)       : 0.163970663018 (M)

****************************************
--> Quench Settings

Quench running as equilibration: FALSE
Number of steps for quenching:  10
QUENCH FREQ  : 1
QUENCH START : 100.00 
QUENCH STEP  : 1.00 
QUENCH END   : 90.00 

****************************************
--> Simulation Components

Chain group 1:
   200 copies of the following chain:
   AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Chain group 2:
   200 copies of the following chain:
   AAAAAAAABBBBBBBBAAAAAAAABBBBBBBBAAAAAAAABBBBBBBBAAAAAAAABBBBBBBB

Chain group 3:
   200 copies of the following chain:
   BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB


****************************************
--> Output Parameters

Print-to-screen frequency    : 10
XTC out frequency            : 50
Energy out frequency         : 25
Overal analysis frequency    : 200
Write chain to chainID file? : False


Keyfile fully parsed! Preparing to start the simulation...
------------------------------------------------------------

SETTING UP THE SIMULATION
............................................................

  [STARTUP]: Using random seed   : 1
  [STARTUP]: Using C random seed : 1
  [STARTUP]: System RAND_MAX     : 2147483647

PARSING PARAMETER FILE...
............................................................

  [WARNING]: Long-range energy check: No defined long-range interaction
             between [A] and [A]. Setting to 0.0
  [STARTUP]: Writing the complete set of parameters used in this
             simulation out to: parameters_used.prm
  [STARTUP]: Simulation started at 2026-07-06 12:35:00.393725

  [STARTUP]: Building initial trajectory and pdb files...
  [STARTUP]: Evaluating initial energy...

  ****************************************
   ENERGY COMPARISON
     STEP             : 0   
     GLOBAL           : -8158880
     SHORT RANGE      : -3421280
     LONG RANGE       : -4737600
     SUPER LONG RANGE : 0
     ANGLES           : 0

  ****************************************
   MEMORY USAGE
     LATTICE GRIDS    :      1.0 MB   (grid + type_grid)
     ENERGY TABLES    :      0.0 MB   (interaction + angle lookup)
     DATA SUBTOTAL    :      1.0 MB
     PROCESS RESIDENT :    973.3 MB   (actual; incl. Python + numpy)
  ****************************************


STARTING SIMULATION
............................................................

Start time: 2026-07-06 12:35:00.393725
  [INFO]:    QUENCH: Updating temperature from 100.000 to 99.000
  [INFO]:    QUENCH: Updating temperature from 99.000 to 98.000
  [INFO]:    QUENCH: Updating temperature from 98.000 to 97.000
  [INFO]:    QUENCH: Updating temperature from 97.000 to 96.000
  [INFO]:    QUENCH: Updating temperature from 96.000 to 95.000
  [INFO]:    QUENCH: Updating temperature from 95.000 to 94.000
  [INFO]:    QUENCH: Updating temperature from 94.000 to 93.000
  [INFO]:    QUENCH: Updating temperature from 93.000 to 92.000
  [INFO]:    QUENCH: Updating temperature from 92.000 to 91.000
  [INFO]:    QUENCH: Updating temperature from 91.000 to 90.000
  [UPDATE]:  Step 10 of 100 [10.000 %] (Energy = -8625520)
  [INFO]:    Reached target temperature of [90.0] - no change
  [UPDATE]:  Step 20 of 100 [20.000 %] (Energy = -9125230)
  [UPDATE]:  Step 30 of 100 [30.000 %] (Energy = -9708940)
  [UPDATE]:  Step 40 of 100 [40.000 %] (Energy = -10039760)
  [UPDATE]:  Step 50 of 100 [50.000 %] (Energy = -10441590)

  ****************************************
   ENERGY COMPARISON
     STEP             : 50   
     GLOBAL           : -10441590
     CURRENT          : -10441590
     DIFFERENCE       : 0
     SHORT RANGE      : -4723760
     LONG RANGE       : -5717830
     SUPER LONG RANGE : 0
     ANGLES           : 0
  ****************************************

  [INFO]:    Writing restart file on step 50...
  [UPDATE]:  Step 60 of 100 [60.000 %] (Energy = -10598700)
  [UPDATE]:  Step 70 of 100 [70.000 %] (Energy = -10915310)
  [UPDATE]:  Step 80 of 100 [80.000 %] (Energy = -11197200)
  [UPDATE]:  Step 90 of 100 [90.000 %] (Energy = -11474840)
  [UPDATE]:  Step 100 of 100 [100.000 %] (Energy = -11725090)

  ****************************************
   ENERGY COMPARISON
     STEP             : 100   
     GLOBAL           : -11725090
     CURRENT          : -11725090
     DIFFERENCE       : 0
     SHORT RANGE      : -5407900
     LONG RANGE       : -6317190
     SUPER LONG RANGE : 0
     ANGLES           : 0
  ****************************************

  [INFO]:    Writing restart file on step 100...

  [INFO]:    Simulation complete
  [INFO]:    Simulation finished at 2026-07-06 12:35:09.136980
  [INFO]:    Simulation time:  0 hours, 0 minutes, 8 seconds

  [INFO]:    Performing final analysis output...
  [INFO]:    Writing restart file on step 100...
  [INFO]:    .... done!
             
             We hope the results are all you hoped for!


/Users/alex/Dropbox/WASHU/Holehouse/tools/PIMMS/pimms/pimms/analysis_structures.py:328: RuntimeWarning: divide by zero encountered in log
  out = np.polyfit(np.log(fitting_separation), np.log(fitting_distances), 1)
