[Wed Jul 12 09:28:55 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0'

Forcefield set to:   pcff+
  File: Local::/home/medea/MD/Jobs/dir0/295/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/dir0/295/pcff+.frc)
		Current system formula: K31Na2Li10Mg206S31Cl393O2892H5536 (K31Na2Li10Mg206S31Cl393O2892H5536)
		The nonbond terms are handled with a cutoff at 9.5 Angstrom.
		The long-range Coulomb interactions are handled with the pppm method to a precision of 0.00001.
		The long-range van der Waals interactions are included via tail corrections.
	
	Stage 2.2: Compress Layer using conjugate gradients and linesearch fast
	                           Target thickness: From cell c dimension
	                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 100 ps 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 on proc 0: Bond atom missing in image check (../domain.cpp:794)
	**************************************

	Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir0/295/pcff+.frc)
		Current system formula: K31Na2Li10Mg206S31Cl393O2892H5536 (K31Na2Li10Mg206S31Cl393O2892H5536)
		The nonbond terms are handled with a cutoff at 9.5 Angstrom.
		The long-range Coulomb interactions are handled with the pppm method to a precision of 0.00001.
		The long-range van der Waals interactions are included via tail corrections.
	
	Stage 2.2: Compress Layer using conjugate gradients and linesearch fast
	                           Target thickness: From cell c dimension
	                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 100 ps with a timestep of 1 fs at temperature 298.2 K
	
An error occurred creating the resulting structure file 2.2.sci: can't use empty string as operand of "-"

can't use empty string as operand of "-"
    while executing
"expr {abs (($v2 - $v1)) / $v1}"
    (object "::compressLayer0" method "::MD::LAMMPS::Stage::Base::xyzToSci" body line 17)
    invoked from within
"::compressLayer0 xyzToSci 2.2.xyz -layer 45.283719500899998"
    ("eval" body line 1)
    invoked from within
"eval ::compressLayer0 $args"
    (procedure "md-lammps-stage-1ff1dd4a-6d89-483e-9d1d-daf1f8993bd5" line 1)
    invoked from within
"$stage xyzToSci $sid.xyz -layer $thickness"
		The minimization finished after 100000 steps ending because the linesearch alpha is zero

Error in stage md-lammps-stage-1ff1dd4a-6d89-483e-9d1d-daf1f8993bd5 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 $args"
    (procedure "md-lammps-stage-1ff1dd4a-6d89-483e-9d1d-daf1f8993bd5" line 1)
    invoked from within
"$stage analyze $sys"

Entire job completed on Wed 12 July 2023 at 09:39:54 CST after 652 s (0:10:52)
and running 1 tasks.