Hello all,
I’m using EMC to build Lammps file (data and params) to run a simulation. First, I’m trying a simple propane example.
My script:
#!/usr/bin/env emc_setup.pl
Chemistry file new style
Options
ITEM OPTIONS
replace true
field opls-ua.prm
ntotal 10000
mass true
density 1
pressure 1
temperature 350
ITEM END
groups
ITEM GROUPS
molecule CCC
ITEM END
I’m executing with perl emc_setup.pl propane.esh and this way I’m getting build.emc file and propane.in (lammps script).
Info: reading script from “./propane.esh”
Info: project = propane
Info: ntotal = 10000
Info: direction = x
Info: shape = 1
Info: force field type = “opls”
Info: force field name = “opls/2012/opls-ua”
Info: force field location = “~/projects/def-ronald/cassiag/v9.4.4/field”
Info: build for LAMMPS script in “…/build”
Info: creating LAMMPS run script “propane.in”
Info: adding pressure sampling
Info: creating EMC build script “build.emc”
When I’m executing build.emc to finally get data and params files (I’m using " ./emc_linux_x86_64 build.emc 2>&1 | tee build.out"
It is appearing this error message:
“Info: script v1.0 started at Mon Jan 22 13:00:41 2024
Info: variables = {seed → -1, ntotal → 10000, fshape → 1, output →
“propane”, field → “opls/2012/opls-ua”, location1 →
“~/projects/def-ronald/cassiag/v9.4.4/field/”, nav → 0.6022141179,
temperature → 350, radius → 5, nrelax → 100, weight_nonbond →
0.0001, weight_bond → 0.0001, weight_focus → 1, cutoff → 9.5,
charge_cutoff → 9.5, kappa → 4, chem_molecule → “CCC”}
Info: output =
{detail → 3, wide → false, expand → false, math → true, reduced →
false, info → true, strict → true, warning → true, message → true,
debug → false, exit → true, ignore → false}
Info: field = {id → opls-ua.prm, mode → opls, style → none, name →
{”~/projects/def-ronald/cassiag/v9.4.4/field/opls/2012/opls-ua.prm",
“~/projects/def-ronald/cassiag/v9.4.4/field/opls/2012/opls-ua.top”},
compress → false, error → true, debug → false, check → {
atomistic → true, charge → true}}
Info: importing ‘~/projects/def-ronald/cassiag/v9.4.4/field/opls/2012/opls-ua.prm’
Info: groups = {ngroups → 1, group →
{id → molecule, chemistry → “CCC”, depth → 8, charges →
forcefield, charge → 0, terminator → false}, ndeletes → 0,
npolymers → 0}
Info: field = {mode → apply, style → none, error → true, debug → false,
check → {atomistic → true, charge → true}}
Info: applying ‘~/projects/def-ronald/cassiag/v9.4.4/field/opls/2012/opls-ua.prm’
Info: variables = {lg_molecule → 3, mg_molecule → 44.0962, ntotal → 0,
mtotal → 0}
Info: simulation = {units → {permittivity → 1, seed → seed}, types → {
coulomb → {pair → {active → true, cutoff → charge_cutoff}}}}
Info: put = {name → “propane”, compress → true, detail → 3}
Info: pdb = {name → “propane”, compress → true, extend → false, mode →
put, system → 0, length → auto, forcefield → opls, atomistic →
full, depth → auto, charges → false, detect → false, atom → index,
residue → index, segment → index, rank → false, hexadecimal →
false, cut → false, pbc → true, map → false, unwrap → clusters,
rigid → true, fixed → true, vdw → false, connectivity → false,
crystal → false, element → auto, parameters → false, flag → {
charge → true, map → true, pbc → true, geometry → true}}
Error: core/systems.c:476 SystemsInit:
Systems not defined.
Program aborted.
Which system is not defined?? I don’t know how to fix it!