It seems that syntax "polymer" doesn't have an option for multiple potentials.
Which is correct, (1) or (2) ??
By the way,
Could I use an user-defined potential (which is not defined in Espresso)?
If so, would anyone let me know how to?
Thank you.
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To simulate LJ + FENE + Harmonic potentials on a polymer chain,
(1)
set monomer_id 0
set monomer_charged_id 1
set bondid_fene 5
set bondid_harmonic 6
inter $monomer_charged_id $monomer_charged_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off
inter $monomer_id $monomer_charged_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off
inter $monomer_id $monomer_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off
inter $bondid_fene fene $fene_k $fene_r
inter $bondid_harmonic harmonic $k_spring $r_eq
polymer $n_polymers $n_monomers $bond_length mode SAW $shield $max_try charge $charge_monomer distance $dist_charge types $monomer_id $monomer_charged_id bond $bondid_fene
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(2)
set monomer_id 0
set monomer_charged_id 1
set bondid_fene 5
set bondid_harmonic 6
inter $monomer_charged_id $monomer_charged_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off
inter $monomer_id $monomer_charged_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off
inter $monomer_id $monomer_id lennard-jones $lj_eps $lj_sig $lj_cut $lj_shift $lj_off
inter $bondid_fene fene $fene_k $fene_r
inter $bondid_harmonic harmonic $k_spring $r_eq
for { set i 0 } { $i < $n_monomers } { incr i } {
if {[expr $i%$dist_charge]==0} {
set ix [expr $box_l*[t_random]]
set iy [expr $box_l*[t_random]]
set iz [expr $box_l*[t_random]]
part $i pos $ix $iy $iz bond $bondid_fene [expr $i+1] q $charge_monomer type $monomer_charged_id
part $i pos $ix $iy $iz bond $bondid_harmonic [expr $i+1] q $charge_monomer type $monomer_charged_id
} else {
set ix [expr $box_l*[t_random]]
set iy [expr $box_l*[t_random]]
set iz [expr $box_l*[t_random]]
part $i pos $ix $iy $iz bond $bondid_fene [expr $i+1] type $monomer_id
part $i pos $ix $iy $iz bond $bondid_harmonic [expr $i+1] type $monomer_id
}
}