./Job.out output for 777: H2O-compress layer 1ns

Status: finished

[Sat May 04 11:39:19 CST 2024] [MD] [warn] 'Starting MedeA Core 3.6.0'

Forcefield set to:   pcff+
  File: Local::/home/medea/MD/Jobs/dir500/777/pcff+.frc 	 md5 sum: 271FB553B535FE0449E31A6F8A0898D3

MedeA version 3.6.0

#-------------------------------------------------------------------------------
#                This calculation has 2 stages
#-------------------------------------------------------------------------------

Stage 1: Variables
	   tstep = 1 fs
	       T = 298.2 K

Stage 2: This LAMMPS calculation has 2 stages:

	Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/777/pcff+.frc)
		Current system formula: O2200H4400 (OH2)
		The nonbond terms are handled with a simple cutoff at 12 Angstrom.
		The long-range van der Waals interactions are included via tail corrections.
		LAMMPS initialized for layer perpendicular to Z.
	
	Stage 2.2: Compress Layer using conjugate gradients and linesearch fast
	                           Target thickness: To final density of 0.997047
	                Relative energy convergence: 0.0
	                          Force convergence: 1.0
	                      Maximum atomic motion: 0.1
	               Maximum number of iterations: 5000
	        Maximum number of force evaluations: 10000
	         Equilibration for 1 ns with a timestep of 1 fs at temperature 298.2 K
	


#-------------------------------------------------------------------------------
#                Running the calculation
#-------------------------------------------------------------------------------

Stage 1: Variables
	   tstep = 1 fs
	       T = 298.2 K

Stage 2: This LAMMPS calculation has 2 stages:

	***** LAMMPS error in LAMMPS.out *****
	ERROR: Domain too large for neighbor bins (../nbin_standard.cpp:133)
	**************************************

	Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/777/pcff+.frc)
		Current system formula: O2200H4400 (OH2)
		The nonbond terms are handled with a simple cutoff at 12 Angstrom.
		The long-range van der Waals interactions are included via tail corrections.
		LAMMPS initialized for layer perpendicular to Z.
	
	Stage 2.2: Compress Layer using conjugate gradients and linesearch fast
	                           Target thickness: To final density of 0.997047
	                Relative energy convergence: 0.0
	                          Force convergence: 1.0
	                      Maximum atomic motion: 0.1
	               Maximum number of iterations: 5000
	        Maximum number of force evaluations: 10000
	         Equilibration for 1 ns with a timestep of 1 fs at temperature 298.2 K
	
		The minimization finished after 11 steps ending because the linesearch alpha is zero

Error in stage md-lammps-stage-compresslayer-c9569cc8-dcc8-4d43-aea0-fb4ab9cc0b60 analyze: invalid command name ""
invalid command name ""
    while executing
"$sys get density"
    (object "::compressLayer0" method "::MD::LAMMPS::Stage::CompressLayer::analyze" body line 116)
    invoked from within
"::compressLayer0 analyze {}"
    ("eval" body line 1)
    invoked from within
"eval ::compressLayer0 $args"
    (procedure "md-lammps-stage-compresslayer-c9569cc8-dcc8-4d43-aea0-fb4ab9..." line 1)
    invoked from within
"$stage analyze $sys"

Entire job completed on Sat 04 May 2024 at 11:39:30 CST after 4 s (0:00:04)
and running 1 tasks.