[Sat Nov 18 15:09:59 CST 2023] [MD] [warn] 'Starting MedeA Core 3.6.0' Forcefield set to: pcff+ File: Local::/home/medea/MD/Jobs/dir500/685/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 P = 1 bar Stage 2: This LAMMPS calculation has 6 stages: Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/685/pcff+.frc) Current system formula: K31Na2Li10Mg206S31Cl393O2892H5536 (K31Na2Li10Mg206S31Cl393O2892H5536) The nonbond terms are handled with a cutoff at 12 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: Minimize using conjugate gradients and linesearch fast Relative energy convergence: 0.0 Force convergence: 1.0 Maximum atomic motion: 0.05 Maximum number of iterations: 3000 Maximum number of force evaluations: 10000 Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs P is 1 bar with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed T is 298.2 K Stage 2.5: NVT integration for 2 ns with a timestep of 1 fs T is 298.2 K Stage 2.6: Custom code -- Custom code reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo 100 fix 1 all nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 all adf 200 4 7 7 0 2.6 0 2.6 fix ad1 all ave/time 1 200000 200000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 all adf 200 6 7 7 0 3.3 0 3.3 fix ad2 all ave/time 1 200000 200000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 all adf 200 3 7 7 0 3.6 0 3.6 fix ad3 all ave/time 1 200000 200000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 200 5 7 7 0 2.8 0 2.8 fix ad4 all ave/time 1 200000 200000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 200 1 7 7 0 3.9 0 3.9 fix ad5 all ave/time 1 200000 200000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 all adf 200 9 7 7 0 4.8 0 4.8 fix ad6 all ave/time 1 200000 200000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 200000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 #------------------------------------------------------------------------------- # Running the calculation #------------------------------------------------------------------------------- Stage 1: Variables tstep = 1 fs T = 298.2 K P = 1 bar Stage 2: This LAMMPS calculation has 6 stages: ***** LAMMPS error in LAMMPS.out ***** ERROR on proc 5: Angle atoms 3374 3372 3373 missing on proc 5 at step 2055639 (../ntopo_angle_all.cpp:64) ************************************** Stage 2.1: Initialize LAMMPS for a Class 2 type of forcefield 'pcff+' (from Local::/home/medea/MD/Jobs/dir500/685/pcff+.frc) Current system formula: K31Na2Li10Mg206S31Cl393O2892H5536 (K31Na2Li10Mg206S31Cl393O2892H5536) The nonbond terms are handled with a cutoff at 12 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: Minimize using conjugate gradients and linesearch fast Relative energy convergence: 0.0 Force convergence: 1.0 Maximum atomic motion: 0.05 Maximum number of iterations: 3000 Maximum number of force evaluations: 10000 Note: 2.2_Minimization.out contains warning messages from LAMMPS - examine this file for additional information. The minimization finished after 36 steps ending because the linesearch alpha is zero Property Value Units ------------------ ---------- ----------- nSteps: 36 Initial Fmax: 32674.0 kJ/mol/Ang Fmax: 10239.7 kJ/mol/Ang Initial Frms: 1782.6 kJ/mol/Ang Frms: 212.5 kJ/mol/Ang P: 14638.6 atm V: 92859.5 Ang^3 rho: 1.3074 g/mL Sxx: -14918.9 atm Syy: -13903.3 atm Szz: -15093.6 atm Syz: 964.7 atm Sxz: 323.4 atm Sxy: 238.3 atm Initial Epot: 495393.3 kJ/mol Epot: -569215.8 kJ/mol a: 33.7899 Ang b: 48.9160 Ang c: 56.1808 Ang alpha: 90.00 degree beta: 90.00 degree gamma: 90.00 degree sum_fx: 0.0 kJ/mol/Ang sum_fy: 0.0 kJ/mol/Ang sum_fz: -0.0 kJ/mol/Ang Stage 2.3: Set the velocities for 298.2 K Stage 2.4: NPT integration for 2 ns with a timestep of 1 fs P is 1 bar with cell dimensions 'a' 'b' 'alpha' 'beta' 'gamma' fixed, others relaxed T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.25 +/- 0.15 K 0 0.0% P: -3 +/- 15 atm 0 0.0% V: 97474 +/- 58 Ang^3 0 0.0% rho: 1.24553 +/- 0.00073 g/mL 0 0.0% Etotal: -651540 +/- 200 kJ/mol 0 0.0% a: 33.7899 +/- 0 Ang 0 0.0% b: 48.916 +/- 0 Ang 0 0.0% c: 58.973 +/- 0.035 Ang 0 0.0% alpha: 90.00022 +/- 0 degree 0 0.0% beta: 90.00022 +/- 0 degree 0 0.0% gamma: 90.00022 +/- 0 degree 0 0.0% Epot: -675090 +/- 190 kJ/mol 0 0.0% Ekin: 23553 +/- 12 kJ/mol 0 0.0% Evdw: 88992 +/- 46 kJ/mol 0 0.0% Ecoul: -764550 +/- 210 kJ/mol 0 0.0% Sxx: 15 +/- 26 atm 0 0.0% Syy: -3 +/- 29 atm 0 0.0% Szz: -3.8 +/- 8.2 atm 0 0.0% Syz: -1 +/- 18 atm 0 0.0% Sxz: 15 +/- 16 atm 0 0.0% Sxy: 4 +/- 19 atm 0 0.0% Stage 2.5: NVT integration for 2 ns with a timestep of 1 fs T is 298.2 K Property Value +/- Uncertainty Units After Steps % Run ------------------ ---------- ----------- ------------- ------------ ------- t: 2000000.0 fs T: 298.204 +/- 0.061 K 0 0.0% P: -87 +/- 19 atm 0 0.0% V: 97735.5 +/- 0 Ang^3 0 0.0% rho: 1.24218 +/- 0 g/mL 0 0.0% Etotal: -651558 +/- 28 kJ/mol 0 0.0% Epot: -675107 +/- 29 kJ/mol 0 0.0% Ekin: 23549.5 +/- 4.8 kJ/mol 0 0.0% Evdw: 88801 +/- 39 kJ/mol 0 0.0% Ecoul: -764362 +/- 60 kJ/mol 0 0.0% Sxx: 93 +/- 26 atm 0 0.0% Syy: 88 +/- 25 atm 0 0.0% Szz: 81 +/- 30 atm 0 0.0% Syz: 0 +/- 15 atm 0 0.0% Sxz: -9 +/- 16 atm 0 0.0% Sxy: -2 +/- 12 atm 0 0.0% Stage 2.6: Custom code -- Custom code reset_timestep 0 thermo_style custom step v_time press vol v_sysdensity temp ebond eangle edihed eimp evdwl ecoul etail elong pe ke thermo 100 fix 1 all nvt temp 298.2 298.2 100 drag 0.0 compute myADF1 all adf 200 4 7 7 0 2.6 0 2.6 fix ad1 all ave/time 1 200000 200000 c_myADF1\[*\] file tmp1.adf mode vector compute myADF2 all adf 200 6 7 7 0 3.3 0 3.3 fix ad2 all ave/time 1 200000 200000 c_myADF2\[*\] file tmp2.adf mode vector compute myADF3 all adf 200 3 7 7 0 3.6 0 3.6 fix ad3 all ave/time 1 200000 200000 c_myADF3\[*\] file tmp3.adf mode vector compute myADF4 all adf 200 5 7 7 0 2.8 0 2.8 fix ad4 all ave/time 1 200000 200000 c_myADF4\[*\] file tmp4.adf mode vector compute myADF5 all adf 200 1 7 7 0 3.9 0 3.9 fix ad5 all ave/time 1 200000 200000 c_myADF5\[*\] file tmp5.adf mode vector compute myADF6 all adf 200 9 7 7 0 4.8 0 4.8 fix ad6 all ave/time 1 200000 200000 c_myADF6\[*\] file tmp6.adf mode vector timestep 1 run 200000 unfix 1 unfix ad1 unfix ad2 unfix ad3 unfix ad4 unfix ad5 unfix ad6 ********************************************* WARNING: this LAMMPS stage completed on Sun 19 November 2023 at 16:39:14 CST after 91748 s (25:29:08) with the following error: ERROR on proc 5: Angle atoms 3374 3372 3373 missing on proc 5 at step 2055639 (../ntopo_angle_all.cpp:64) ********************************************* Entire job completed on Sun 19 November 2023 at 16:39:14 CST after 91748 s (25:29:08) and running 1 tasks.