problems with END to END distance of polymer

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1

Hi LAMMPS users,

i would like to comput end-to-end length of a polymer using LAMMPS directly.

I use this formulation:

variable end_to_end equal sqrt((x[${id1}] - x[${id0}])^2 + (y[$[id1}] -y[${id0}])^2 + (z[${id1}] - z[${id0}])^2)


fix 2 all print 1 "${step} ${end_to_end}" file ../thermo-data-MD/end_to_end.log title "End to End Distance of PCE23-6: step End to End" screen no




but i obtain this error:

<b>ERROR on proc 1: Substitution for illegal variable (input.cpp:414)
ERROR on proc 2: Substitution for illegal variable (input.cpp:414)
ERROR on proc 3: Substitution for illegal variable (input.cpp:414)
ERROR on proc 4: Substitution for illegal variable (input.cpp:414)
ERROR on proc 5: Substitution for illegal variable (input.cpp:414)
ERROR on proc 6: Substitution for illegal variable (input.cpp:414)
ERROR on proc 7: Substitution for illegal variable (input.cpp:414)
ERROR on proc 8: Substitution for illegal variable (input.cpp:414)
ERROR on proc 9: Substitution for illegal variable (input.cpp:414)
ERROR on proc 10: Substitution for illegal variable (input.cpp:414)
ERROR on proc 11: Substitution for illegal variable (input.cpp:414)
ERROR on proc 12: Substitution for illegal variable (input.cpp:414)
ERROR on proc 13: Substitution for illegal variable (input.cpp:414)
ERROR on proc 14: Substitution for illegal variable (input.cpp:414)
ERROR on proc 15: Substitution for illegal variable (input.cpp:414)
Nlocal:    16 ave 122 max 0 min
Histogram: 12 1 0 1 0 1 0 0 0 1
Nghost:    29.75 ave 151 max 0 min
Histogram: 10 0 1 2 1 0 1 0 0 1
Neighs:    416.375 ave 3677 max 0 min
Histogram: 12 1 1 1 0 0 0 0 0 1

Total # of neighbors = 6662
Ave neighs/atom = 26.0234
Ave special neighs/atom = 5.57812
Neighbor list builds = 0
Dangerous builds = 0
ERROR on proc 0: Substitution for illegal variable (input.cpp:414)</b>

where I’m wrong?

2

Hi LAMMPS users,

i would like to comput end-to-end length of a polymer using LAMMPS directly.

I use this formulation:

variable end_to_end equal sqrt((x[\{id1\}\] \- x\[{id0}])^2 + (y[\[id1\}\] \-y\[{id0}])^2 + (z[\{id1\}\] \- z\[{id0}])^2)

fix 2 all print 1 "\{step\} {end_to_end}" file
../thermo-data-MD/end_to_end.log title "End to End Distance of PCE23-6: step
End to End" screen no

but i obtain this error:

ERROR on proc 1: Substitution for illegal variable (input.cpp:414)
ERROR on proc 2: Substitution for illegal variable (input.cpp:414)
ERROR on proc 3: Substitution for illegal variable (input.cpp:414)
ERROR on proc 4: Substitution for illegal variable (input.cpp:414)
ERROR on proc 5: Substitution for illegal variable (input.cpp:414)
ERROR on proc 6: Substitution for illegal variable (input.cpp:414)
ERROR on proc 7: Substitution for illegal variable (input.cpp:414)
ERROR on proc 8: Substitution for illegal variable (input.cpp:414)
ERROR on proc 9: Substitution for illegal variable (input.cpp:414)
ERROR on proc 10: Substitution for illegal variable (input.cpp:414)
ERROR on proc 11: Substitution for illegal variable (input.cpp:414)
ERROR on proc 12: Substitution for illegal variable (input.cpp:414)
ERROR on proc 13: Substitution for illegal variable (input.cpp:414)
ERROR on proc 14: Substitution for illegal variable (input.cpp:414)
ERROR on proc 15: Substitution for illegal variable (input.cpp:414)
Nlocal: 16 ave 122 max 0 min
Histogram: 12 1 0 1 0 1 0 0 0 1
Nghost: 29.75 ave 151 max 0 min
Histogram: 10 0 1 2 1 0 1 0 0 1
Neighs: 416.375 ave 3677 max 0 min
Histogram: 12 1 1 1 0 0 0 0 0 1

Total # of neighbors = 6662
Ave neighs/atom = 26.0234
Ave special neighs/atom = 5.57812
Neighbor list builds = 0
Dangerous builds = 0
ERROR on proc 0: Substitution for illegal variable (input.cpp:414)

where I'm wrong?

how should we know? the input you provide is incomplete and people
here don't have crystal balls or can read minds...

axel.

3

May it be spaces in the "equal" string?

There is also a square bracket instead of a curly one in y[$[id1}]

Oleg.

4

Hi LAMMPS users,

i would like to comput end-to-end length of a polymer using LAMMPS directly.

I use this formulation:

clear
units real
atom_style full
dimension 3
boundary p p p

neighbor 2.5 bin
neigh_modify every 1 delay 0 check yes

# -----------------------------------------------------------
# – Force Field styles -------------------------------------
# -----------------------------------------------------------
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style umbrella

# style cutoff1 cutoff2
pair_style lj/cut/coul/cut 9.0 10.5

pair_modify mix arithmetic
#Modify the parameters of the currently defined pair style
#mix arithmetic
#epsilon_ij = sqrt(epsilon_i * epsilon_j)
#sigma_ij = (sigma_i + sigma_j) / 2

dielectric 1

special_bonds dreiding # oppure questo lj 0.0 0.0 1.0
#Set weighting coefficients for pairwise energy and force contributions between pairs of atoms that are also permanently bonded
#to each other, either directly or via one or two intermediate bonds.
#The dreiding keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both LJ and Coulombic interactions, which is the default for
#the Dreiding force field, as discussed in (Mayo).

# -----------------------------------------------------------
# ----------------- Atom Definition Section -----------------
# -----------------------------------------------------------
read_data …/common/system.data

# -----------------------------------------------------------
# ----------------- Settings Section ------------------------
# -----------------------------------------------------------
# bond-type k r0
bond_coeff 1 350.0 1.090 # H_ C_3
bond_coeff 2 350.0 1.530 # C_3 C_3
bond_coeff 3 350.0 1.430 # C_3 C_2
bond_coeff 4 350.0 1.420 # C_3 O_3
bond_coeff 5 350.0 1.320 # C_2 O_3
bond_coeff 6 350.0 1.220 # C_2 O_2

# angle-type k theta0
angle_coeff 1 50.0 109.4710 # X C_3 X
angle_coeff 2 50.0 120.0000 # X C_2 X
angle_coeff 3 50.0 104.5100 # X O_3 X

# dihedral-type k d n
dihedral_coeff 1 1.0 -1 3 # X C_3 C_3 X
dihedral_coeff 2 0.5 -1 6 # X C_3 C_2 X
dihedral_coeff 3 0.5 -1 6 # X C_2 O_3 X
dihedral_coeff 4 2.5 -1 2 # X C_2 O_2 X
dihedral_coeff 5 1.0 -1 3 # X C_3 O_3 X

# improper-type k omega0
improper_coeff 1 40.0 0.0 # C_2 X X X

# atom-type atom-type epsilon sigma cutoff L-J
pair_coeff 1 1 0.0152 2.8464 7.1160
pair_coeff 2 2 0.0951 3.4729 8.68225
pair_coeff 3 3 0.0951 3.4729 8.68225
pair_coeff 4 4 0.0957 3.0331 7.58275
pair_coeff 5 5 0.0957 3.0331 7.58275
pair_coeff 6 6 0.5000 2.8009 7.00225