Hi,
I am using “lammps-29Sep10” windows binary executable to test the use of tabular potentials.
when I followed the manual and created the potential file for a simple harmonic function for two atom model.
I am getting unusual errors as given.
The details are give below the files (a) in.test (b) test.lammps © potential tabular file (d) output
(a) in.test file
units real
atom_style full
boundary p p p
bond_style table linear 10000
atom_modify sort values 1.0
read_data test.lammps
neighbor 2.0 bin
neigh_modify delay 5
timestep 1.0
min_style cg
min_modify dmax 0.2
minimize 1.0e-4 1.0e-6 10000 100000
thermo 100
thermo_style custom step temp vol press ke pe etotal pxy pxz pyz
fix 1 all nvt temp 293.0 293.0 100.0
dump 1 all atom 2000 dump.lammpstrj
run 25000
(b) test.lammps file
2 atoms
1 bonds
0 angles
0 dihedrals
0 impropers
1 atom types
1 bond types
0 angle types
0 dihedral types
0 improper types
0.0 5.0 xlo xhi
0.0 5.0 ylo yhi
0.0 5.0 zlo zhi
Masses
1 15.0
Bond Coeffs
1 bond.table bond
Atoms
1 1 1 0.0000 1.00 5.00 4.00
2 1 1 0.0000 2.00 5.00 4.00
Bonds
1 1 1 2
creating the table in Matlab
r=0:1e-3:10.0;
U = 0.5 * 899.95759 * (r-1.54).^2;
F = - 0.5 * 899.95759 * 2 * (r-1.54);
gives the table
© bond.table
bond Potential for butane
bond_butane
N 10001
1.0000000e+000 0.0000000e+000 1.0671697e+003 1.3859347e+003
2.0000000e+000 1.0000000e-003 1.0657842e+003 1.3850347e+003
…
…
…
9.9980000e+003 9.9970000e+000 3.2182865e+004 -7.6109413e+003
9.9990000e+003 9.9980000e+000 3.2190477e+004 -7.6118413e+003
1.0000000e+004 9.9990000e+000 3.2198089e+004 -7.6127413e+003
1.0001000e+004 1.0000000e+001 3.2205702e+004 -7.6136412e+003
(d) When I run (output)
Scanning data file …
1 = max bonds/atom
Reading data file …
orthogonal box = (0 0 0) to (5 5 5)
1 by 1 by 1 processor grid
2 atoms
1 bonds
Finding 1-2 1-3 1-4 neighbors …
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
WARNING: Resetting reneighboring criteria during minimization
Setting up minimization …
Memory usage per processor = 2.09904 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 0 -1.#IND -1.#IND -1.#IND
Thanks
srinivas
