Hi,
I am trying to run a simulation with an already equilibrated structure in a box that is enough space for additional atoms, but when I try to extend the box dimensions a get the following error for LAMMPS:
Setting up run …
WARNING: Inconsistent image flags (…/domain.cpp:645)
Memory usage per processor = 8.72688 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -2834.819 1099.2163 -1542.7443 -2045.3261
ERROR on proc 10: Bond atoms 484 485 missing on proc 10 at step 290 (…/neigh_bond.cpp:65)
ERROR on proc 9: Bond atoms 394 395 missing on proc 9 at step 290 (…/neigh_bond.cpp:65)
APPLICATION TERMINATED WITH THE EXIT STRING: Terminated (signal 15)
The only change in my box dimensions are shown below
-0.0203835 18.6204 xlo xhi
-0.0203835 18.6204 ylo yhi
-0.0203835 18.6204 zlo zhi
to
-0.0203835 18.6204 xlo xhi
-0.0203835 18.6204 ylo yhi
-0.0203835 37.2408 zlo zhi
I can run a simulation with the first set of dimensions but the second yields the error. How could I run a simulation with water in a box larger than the equilibrated structure? My input file is below…My ultimate goal is to equilibrate H2O with SiC to calculate the equilibrium properties of the interface between the two structures. Thanks
INPUT FILE
#TIP4P/2005f model: M. A. González and J. L. F. Abascal, A flexible
#model for water based on TIP4P/2005, J. Chem. Phys. 135 (2011) 224516.
#variables-------------------------------------------------------------------------
variable Text equal 100.0
variable Pext equal 0.0
variable Nrun equal 100000
variable Nrun1 equal 50000
variable Nrun2 equal 150000
variable ts equal 0.2
variable Tdamp equal ${ts}*100
variable Pdamp equal ${ts}*1000
variable Nf equal ${Nrun}/100
variable Ne equal 10
variable Nr equal {Nf}/{Ne}
variable Ndump equal ${Nrun}/2
variable Nr_rdf equal 0.5*{Nrun}/{Ne}
variable watMoleMass equal 18.0153 # /(g/mol)
variable nAvog equal 6.0221415e23 # Avogadro’s number
variable watMoleculeMass equal ({watMoleMass}/{nAvog}) # /(g/molecule)
variable A3_in_cm3 equal 1e-24 # Angstrom^3 in cm^3
variable nAtoms equal atoms
variable nMolecules equal v_nAtoms/3
units real
dimension 3
boundary p p p
atom_style full
read_data H2O_648N_Coord.txt
#create groups ###---------------------------------------------------------
mass 1 1.00794 # H
mass 2 15.9994 # O
#include forcefield.TIP4P-2005.txt
TIP4P/2005 potential parameters-------------------------
group O type 2
group H type 1
group H2O type 1 2
TIP4P/2005 flexible potenrial parameters---------------------------------
pair_style lj/cut/tip4p/long 2 1 1 1 0.1546 14.0
kspace_style pppm/tip4p 1e-5
pair_coeff 1 1 0.0 0.0
pair_coeff 1 2 1 0.0 1.5795
pair_coeff 2 2 0.1852573718 3.1644
bond_style morse
bond_coeff 1 103.38934 2.287 0.9419
angle_style harmonic
angle_coeff 1 43.95435 107.4
neighbor-----------------------------------------------------------------
neighbor 2.0 bin
neigh_modify delay 0 every 1 check yes
initial condition------------------------------------------------------
velocity all create 100 1234546 dist gaussian mom yes rot yes
#dumps and restart-----------------------------------------------------------
dump waterdump all custom 1000 flex.lammpstrj id type x y z vx vy vz
dump trj all atom ${Nf} WaterTrj.data
dump_modify trj scale no sort id
dump deqlb all atom ${Nrun} FinalCoord.data
dump_modify deqlb scale no sort id
dump coord all custom ${Ndump} DumpCoord.xyz element x y z
#dump_modify coord element H O
#dump_modify deqlb element H O
restart 200000 t.restart1 t.restart2
timestep ${ts}
fix 2 all nvt temp 1 ${Text} 250
run ${Nrun1}
unfix 2
fix 3 all nvt temp {Text} {Text} 250
run ${Nrun2}
unfix 3
fix 4 all npt iso {Pext} {Pext} {Pdamp} temp {Text} {Text} {Tdamp}
variable Dens equal v_nMolecules*{watMoleculeMass}/(vol*{A3_in_cm3})
fix DensAve all ave/time {Ne} {Nr} ${Nf} v_Dens file wat.dens.data
compute bonds all property/local btype batom1 batom2
compute angles all property/local atype aatom1 aatom2 aatom3
compute vel H2O property/atom vx vy vz
#dumps
dump bonds all local ${Ndump} dump.bond.txt c_bonds[1] c_bonds[2] c_bonds[3]
dump angles all local ${Ndump} dump.angle.txt c_angles[1] c_angles[2] c_angles[3] c_angles[4]
output-------------------------------------------------------------------
thermo_style custom step temp pe ke etotal press vol lx
thermo_modify flush yes norm yes
thermo ${Nf}
run ${Nrun}
dump velocities H2O custom ${Nf} Velocities.txt c_vel[2]
write_restart restart.TIP4P_1procs_0.2fs_648N_100K