Hi, this is my first time using EMC, and I’ve met some problems here.
I’m trying to make a semicrystalline bulk such as the image in the emc homepage.
It seems like both sides are crystalline and amorphous in the middle.
when making the structure before running emc simulation, is the SMILES notation only to build it?
Or is there an other way to build the structure?
I also want to build this semicrystalline model, but I find it is not easy. If I understand correctly. We need to build a crystalline model first, cut some bonds and remove some sites, and do the EMC.
Dear User,
The picture on the home page depicts a coarse-grained (CG) two-phase liquid-liquid equilibrium (LLE) system created for dissipative particle dynamics (DPD). An atomistic example on how to generate multiple phases can be found under
examples/setup/chemistry/multiphase
Multiple phases are controlled by the phases option. It works the same no matter the type of simulation length scale you use (CG or atomistic). For generating semicrystalline polyethylene, you can use
examples/build/polymer/polyethylene/build.emc
as a starter. You will need to use this directly with EMC and not with EMC Setup. I would suggest copying this file to a separate clean directory and execute EMC as follows
emc.sh build.emc
in this directory.
Thank you for your reply!
I’ve tried the one that you suggested, to copy the polyethylene and execute emc.sh build.emc
It shows the same error that there is no terminator indicating methyl.
Should I change the build.emc file to fix this?
The imported polyethylene.emc is as follow:
(* EMC: Enhanced Monte Carlo simulations *)
(*
file: polyethylene.emc
author: Pieter J. in 't Veld
date: February 8, 2006
purpose: description of crystalline unit cell of polyethylene using
P.J. in 't Veld et al., Macromolecules 2006, 39, 439,
which results in atmospheric pressure at T = 402K.
*)
identity = {name → “polyethylene”};
units = {type → atomistic, length → 1, energy → 1};
variables = {alpha → 1.208435, phi → 0.733, lbond → 1.53, factor → 1.53/lbond, la → 7.7479factor, lb → 4.4626factor, lc → 2.51822*factor, sigma → 4.009044232, nsites → 4, nclusters → 2};
constants = {clusters → {polyethylene}, groups → {methylene, methyl}, sites → {ch2, ch3}};
types = {atomistic → united,
mass → {n → 2, data → {
{id → ch2, element → “C”, reference → 0, mass → 14},
{id → ch3, element → “C”, reference → 1, mass → 15}}},
standard → {
active → true,
pair → {active → true, mix → berthelot, n → 3, data → {
{ch2, ch2, 0.0934, sigma, 2.5sigma},
{ch3, ch3, 0.2265, sigma, 2.5sigma}}},
bond → {active → true, n → 2, data → {
{ch2, ch2, 899, 1.53},
{ch2, ch3, 899, 1.53}}},
angle → {active → true, n → 3, data → {
{ch2, ch2, ch2, 120, 112},
{ch2, ch2, ch3, 120, 112},
{ch3, ch2, ch3, 120, 112}}},
torsion → {active → true, n → 3, data → {
{ch2, ch2, ch2, ch2, 3, {
{0.8, 1, 0}, {0.4335, 2, 180}, {1.62, 3, 0}}},
{ch2, ch2, ch2, ch3, 3, {
{0.8, 1, 0}, {0.4335, 2, 180}, {1.62, 3, 0}}},
{ch3, ch2, ch2, ch3, 3, {
{0.8, 1, 0}, {0.4335, 2, 180}, {1.62, 3, 0}}}}}}};
groups = {
n → 2, data → {
{group → methylene, name → “METHYLENE”, terminator → false,
chemistry → “C”, nsites → 1,
sites → {
site → 0, mass → ch2, charge → 0, connects → {branch, branch},
bonds → {single, single}},
nbranches → 1,
branches → {site → 0, nconnects → 2,
connects → {{methylene, 0}, {methyl, 0}}}},
{group → methyl, name → “METHYL”, terminator → true,
chemistry → “*C”, nsites → 1,
sites → {
site → 0, mass → ch3, charge → 0, connects → {branch},
bonds → single},
nbranches → 1,
branches → {site → 0, nconnects → 1,
connects → {methylene, 0}}}}};
systems = {
n → 1, properties → {
id → 0, p → 0, v → lalblc, t → 298.15, mass → 56,
nsites → 4, nclusters → 2, geometry → {la, lb, lc, 0, 0, 0}}};
clusters = {
n → 2, data → {
{cluster → 0, id → polyethylene, head → 0, tail → 1, flags → 0b0001},
{cluster → 1, id → polyethylene, head → 2, tail → 3, flags → 0b0001}}};
sites = {
n → 4, data → {
{site → 0, cluster → 0, system → 0, mass → ch2, flags → 0b0100,
group → {methylene, 0}, connects → {1, 1, -1, -1}, p → {
la/4-lbondcos(phi)sin(alpha/2)/2,
lb/4+lbondsin(alpha/2)sin(phi)/2,
lc/4},
xtal → {{0, 0, -1}, {0, 0, 0}}},
{site → 1, cluster → 0, system → 0, mass → ch2, flags → 0b1000,
group → {methylene, 0}, connects → {0, 0, -1, -1}, p → {
la/4+lbondcos(phi)sin(alpha/2)/2,
lb/4-lbondsin(alpha/2)sin(phi)/2,
3lc/4},
xtal → {{0, 0, 0}, {0, 0, 1}}},
{site → 2, cluster → 1, system → 0, mass → ch2, flags → 0b0100,
group → {methylene, 0}, connects → {3, 3, -1, -1}, p → {
3la/4-lbondcos(phi)sin(alpha/2)/2,
3lb/4-lbondsin(alpha/2)sin(phi)/2,
lc/4},
xtal → {{0, 0, -1}, {0, 0, 0}}},
{site → 3, cluster → 1, system → 0, mass → ch2, flags → 0b1000,
group → {methylene, 0}, connects → {2, 2, -1, -1}, p → {
3la/4+lbondcos(phi)sin(alpha/2)/2,
3lb/4+lbondsin(alpha/2)sin(phi)/2,
3lc/4},
xtal → {{0, 0, 0}, {0, 0, 1}}}}};
I guess the line
connects → {{methylene, 0}, {methyl, 0}} is the problem.
Dear users,
To close the loop on this topic: I uploaded a new version for EMC v9.4.4_20230801 (see https://sourceforge.net/projects/montecarlo/files/), which solves the issue as discussed in this thread. Please use the following build file:
build.emc (3.3 KB)
Please note two additions:
merge -> true to the crystal command in line 28, which enables merging of unit cell clusters into super clusters,types -> {applied -> true} to the simulation command in lines 61-63, which indicates, that the provided force field parameters are valid and the systems have been typed.