Dear Lammps User,
When I am simulating my input file I am getting the following error
ERROR on proc 0: Angle atoms 14337 14336 14338 missing on proc 0 at step 5 (src/ntopo_angle_partial.cpp:69)
Last command: run 40000
My input file is as shown below:
units real
dimension 3
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
read_data 4nmPore.data
#read_restart 3nmPore-200000.restart
group ca type 1
group ox type 2
group hy type 3
group wo type 4
group wh type 5
group hydroxid type 2 3
group ca-o type 1 2
group spc type 4 5
group portlandite type 1 2 3
#delete_atoms group portlandite
pair_style lj/cut/coul/long 10
pair_coeff 1 1 5.0298e-6 5.5617 # ca-ca
pair_coeff 1 2 8.841e-4 4.3636 # ca-o port
pair_coeff 2 2 0.1554 3.1655 # o-o port
pair_coeff 2 3 0.0 0.0 # o-h port
pair_coeff 3 3 0.0 0.0 # h-h port
pair_coeff 4 4 0.1554 3.1655 # o-o water
pair_coeff 5 5 0.0 0.0 # h-h water
pair_coeff 2 4 0.1554 3.1655 # o-o port-water
pair_coeff 1 4 0.0777 4.19586 # ca-o port-water
pair_coeff 1 5 0.0 0.0 # ca-h port-water
pair_coeff 2 5 0.0 1.5827 # o-h port-water
pair_coeff 3 4 0.0 1.5827 # h-h port-water
pair_coeff 3 5 0.0 0.0 # o-h water
bond_style harmonic
bond_coeff 1 554.1349 1.0 # o-h port
bond_coeff 2 554.1349 1.0 # o-h water
angle_style harmonic
angle_coeff 1 30.0 109.47 # ca-o port
angle_coeff 2 45.7696 109.47 # o-h water
#velocity all create 300.0 104112 dist gaussian # From Cygan et.al
#minimize 1.0e-4 1.0e-6 100 1000
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes one 3000
variable dz equal 0.2
variable zlow equal zlo
variable zhigh equal zhi
compute 5 all ke # Kinetic energy for all the atoms
compute 6 all pe # Potential energy for all the atoms
compute myTemp all temp # Temperature of all the atoms
#compute RDFHydroxidNVT hydroxid rdf 50
region pore block EDGE EDGE EDGE EDGE EDGE EDGE
#delete_atoms group portlandite
fix constrain spc shake 1.0e-4 100 0 b 1 a 1
#fix 2 portlandite setforce 0.0 0.0 0.0
fix 1 all nvt temp 300.0 300.0 500
#fix_modify 1 temp myTemp
fix 5 all ave/time 1 1 500 c_5 file ek.txt
fix 6 all ave/time 1 1 500 c_6 file ep.txt
fix 7 all ave/time 1 1 500 c_myTemp file T.txt
#fix avrdf3 hydroxid ave/time 1 1 10000 c_RDFHydroxidNVT file rdfHydroxid-17-2-15.txt mode vector
#fix densityWaterNVT spc ave/spatial 1 100 100000 z lower {dz} density/mass region pore file densityProfileWater.txt
#fix densityHNVT wh ave/spatial 1 100 100000 z lower {dz} density/mass region pore file densityProfileHydrogen.txt
#fix densityOxNVT wo ave/spatial 1 100 100000 z lower ${dz} density/mass region pore file densityProfileOxygen.txt
thermo 100
thermo_style custom step c_myTemp
thermo_modify norm no flush yes
dump NVTDump all custom 50 water-.txt id type mol x y z vx vy vz
restart 100000 4nmPore-.restart # Remember to collect these in the bash script
timestep 1.0
run 40000
Let me also know if there is any mistake in my input file.
Regards,
Rajneesh
IIT Mandi (H.P)