"ERROR: Not all per-type masses are set" when using molecule command inserting TIP4P water molecule

Hi,
There is a Ni0(H2O)2 molecule in box, the force field used for define it is UFF4MOF.
The data file is generated by lammps_interface and can run MD using lammps successfully.
Now I want to fill the box with TIP4P-Ew H2O molecules, and I use molecule and creat_atomscommand.

  1. The script run into an ERROR says "ERROR: Not all per-type masses are set". I’ve checked the input script carefully but can’t find out why, please help me.
  2. How to define the interaction between TIP4P-Ew H2O molecules and Ni0(H2O)2 since they are defined in different force field?

I am using lammps-11Aug17 and below is my input script.

Thanks a lot!

Zhongming


#content: in.H2O2-Ni0

log             log.H2O2-Ni0 append

units           real

atom_style      full

boundary        p p p

pair_style      hybrid lj/cut/coul/long 12.500 lj/cut/tip4p/long 9 10 9 16 0.1250 12.500 10.000

bond_style      harmonic

angle_style     hybrid fourier cosine/periodic harmonic 

kspace_style    ewald 0.000001

dielectric      1.0

pair_modify     pair lj/cut/coul/long tail yes mix arithmetic

special_bonds   lj/coul 0.0 0.0 1.0

box tilt        large

read_data       data.H2O2-Ni0 extra/atom/types 2 extra/bond/types 1 extra/angle/types 1

# insert TIP4P-Ew H2O

molecule h2o H2O.txt offset 3 2 3 0 0

create_atoms 0 random 20 1 NULL mol h2o 1

# add coffs for TIP4P-Ew H2O according to http://lammps.sandia.gov/doc/Section_howto.html#tip4p-water-model

pair_coeff 4 4 lj/cut/tip4p/long 0.16275 3.16435

pair_coeff 4 5 lj/cut/tip4p/long 0.0 0.0

pair_coeff 5 5 lj/cut/tip4p/long 0.0 0.0

bond_coeff 3 559.995206 0.9572

angle_coeff 4 harmonic 300.0 104.52

dump myDump1 all atom 1 dump1.txt

velocity all create 298.0 12345689 dist uniform 

neighbor 2.0 bin

neigh_modify delay 0 every 10 check yes

thermo      200

thermo_style custom step time temp

thermo_modify norm no flush yes

fix 1 all nvt temp 298.0 298.0 100.0 

minimize 1.0e-8 1.0e-8 10000 10000 

# output trj

dump trj2 all xyz 4000 MD-result.xyz

dump_modify trj2 element Zr C O O H Ni O H

timestep 0.5

run 200000 # run md for 0.1ns


# content: data.H2O2-Ni0

Created on Sat Mar 10 15:52:15 2018 

           7 atoms

           6 bonds

           7 angles

           3 atom types

           2 bond types

           3 angle types

           0.000000  30.000000 xlo xhi

           0.000000  30.000000 ylo yhi

           0.000000  30.000000 zlo zhi

           0.000000   0.000000   0.000000 xy xz yz

Masses

    1    58.693400000 # Ni1

    2    15.999400000 # O_3

    3     1.007940000 # H_

Bond Coeffs

    1      272.490300        1.895541  # Ni1 O_3

    2      559.995206        0.990254  # O_3 H_

Angle Coeffs

    1              cosine/periodic       17.945113               1               1 # O_3 Ni1 O_3

    2                      fourier       57.090081        0.300235        0.267331        0.266745 # Ni1 O_3 H_

    3                      fourier      122.883342        0.300235        0.267331        0.266745 # H_ O_3 H_

Pair Coeffs

    1     lj/cut/coul/long   0.015000        2.524807 # Ni1 Ni1

    2     lj/cut/coul/long   0.060000        3.118146 # O_3 O_3

    3     lj/cut/coul/long   0.044000        2.571134 # H_ H_

Atoms

       1        1        1     0.00000   -6.51360   -3.19770    5.43240

       2        1        2     0.00000   -8.00880   -3.22170    6.57150

       3        1        3     0.00000   -7.67370   -3.33060    7.48860

       4        1        3     0.00000   -8.50470   -4.04940    6.38790

       5        1        2     0.00000   -5.04570   -3.16620    4.25970

       6        1        3     0.00000   -4.88910   -2.22900    4.01040

       7        1        3     0.00000   -4.25640   -3.42000    4.78620

Bonds

       1        1        1        2

       2        1        1        5

       3        2        2        3

       4        2        2        4

       5        2        5        6

       6        2        5        7

Angles

       1        1        2        1        5

       2        2        1        2        3

       3        3        3        2        4

       4        2        1        2        4

       5        2        1        5        6

       6        3        6        5        7

       7        2        1        5        7


# content: H2O.txt

Created on Sat Mar 10 09:43:39 2018 

           3 atoms

           2 bonds

           1 angles

Coords

       1        8.17610    0.16360    0.10430 # O

       2        8.85210    0.64630    0.64340 # H

       3        7.32070    0.61450    0.31730 # H

Types

       1 1

       2 2

       3 2

Masses

    1    15.9994 # O

    2     1.008 # H

    3     1.008 # H

Charges

    1   -1.0484

    2   0.5242

    3   0.5242

Bonds

       1        1        1        2

       2        1        1        3

Angles

       1        1        2        1        3


# content :  log.lammps

units           real

atom_style      full

boundary        p p p

# for lj/cut/tip4p: LJ cutoff >= Coulomb cutoff + 2*(OM distance)

pair_style      hybrid lj/cut/coul/long 12.500 lj/cut/tip4p/long 9 10 9 16 0.1250 12.500 10.000

bond_style      harmonic

angle_style     hybrid fourier cosine/periodic harmonic

kspace_style    ewald 0.000001

dielectric      1.0

pair_modify     pair lj/cut/coul/long tail yes mix arithmetic

special_bonds   lj/coul 0.0 0.0 1.0

box tilt        large

read_data       data.H2O2-Ni0 extra/atom/types 2 extra/bond/types 1 extra/angle/types 1

  triclinic box = (0 0 0) to (30 30 30) with tilt (0 0 0)

  2 by 2 by 2 MPI processor grid

  reading atoms ...

  7 atoms

  scanning bonds ...

  2 = max bonds/atom

  scanning angles ...

  3 = max angles/atom

  reading bonds ...

  6 bonds

  reading angles ...

  7 angles

  3 = max # of 1-2 neighbors

  4 = max # of 1-3 neighbors

  6 = max # of special neighbors

#### Atom Groupings ####

group           1        id   1:7

7 atoms in group 1

#### END Atom Groupings ####

# insert H2O

molecule h2o H2O.txt offset 3 2 3 0 0

Read molecule h2o:

  3 atoms with 5 types

  2 bonds with 3 types

  1 angles with 4 types

  0 dihedrals with 0 types

  0 impropers with 0 types

create_atoms 0 random 20 1 NULL mol h2o 1

WARNING: Molecule attributes do not match system attributes (../molecule.cpp:1369)

Created 60 atoms

# add coffs for h2o according to http://lammps.sandia.gov/doc/Section_howto.html#tip4p-water-model

pair_coeff 4 4 lj/cut/tip4p/long 0.16275 3.16435

pair_coeff 4 5 lj/cut/tip4p/long 0.0 0.0

pair_coeff 5 5 lj/cut/tip4p/long 0.0 0.0

bond_coeff 3 559.995206 0.9572

angle_coeff 4 harmonic 300.0 104.52

dump myDump1 all atom 1 dump1.txt

velocity all create 298.0 12345689 dist uniform

ERROR: Not all per-type masses are set (../velocity.cpp:63)

Last command: velocity all create 298.0 12345689 dist uniform

in.H2O2-Ni0 (1.5 KB)

data.H2O2-Ni0 (2.09 KB)

H2O.txt (558 Bytes)

log.H2O2-Ni0 (1.83 KB)

Hi,
There is a Ni0(H2O)2 molecule in box, the force field used for define it is
UFF4MOF.
The data file is generated by lammps_interface and can run MD using lammps
successfully.
Now I want to fill the box with TIP4P-Ew H2O molecules, and I use molecule
and creat_atomscommand.

The script run into an ERROR says "ERROR: Not all per-type masses are set".
I’ve checked the input script carefully but can’t find out why, please help
me.

you are telling LAMMPS with the read_data command to reserve two
additional atom types. however, the data file will not contain their
masses and you don't set them anywhere. hence the error message.

How to define the interaction between TIP4P-Ew H2O molecules and Ni0(H2O)2
since they are defined in different force field?

this is a problem. you can try one of the mixing rules, but for the
most accurate result, you have to have parameters that are
consistently parameterized together.

axel.

p.s.: there is no need to use a hybrid pair style here, just using
lj/cut/tip4p/long is sufficient.