Kateryna Goloviznina
Agilio Padua
-
polarizer.py: add Drude induced dipoles to LAMMPS data files. -
scaleLJ.py: scales pair coefficients of Lennard-Jones interactions. -
coul_tt.py: adds Tang-Toennies charge-dipole damping for densely charged atoms. -
alpha.ff: Drude parameter database. -
fragment.ff: fragment database. -
fragment_topologies/: structure files for typical IL fragments. -
example_il/: examples of [C4C1im][DCA] molecule files and force field database (aprotic ionic liquid). -
example_pil/: examples of ethylammonium nitrate (EAN) molecule files and force field database (protic ionic liquid). -
example_des/: examples of choline chloride:ethylene glycol (ChCl:EG) molecule files and force field database (deep eutectic solvent).
Download the files or clone the repository:
git clone https://github.com/paduagroup/clandpol.git
These are instructions on how to build an initial configuration for a polarisable system composed of molecules, ions or materials.
To perform the simulation of a polarisable system, the USER-DRUDE package should be enabled during LAMMPS compilation.
Two systems, 1-butyl-3-methylimidazolium dicyanamide ([C4C1im][DCA]) and ethylammonium nitrate (EAN), are given as examples of aprotic and protic ionic liquids, respectively.
The input files for a system consisting of one [C4C1im]+ cation and one [DCA]- anion can be found in the example_il/ folder.
Use fftool to create data.lmp, in.lmp and pair.lmp files. A separate pair.lmp file containing all i-j pair coefficients will be required later and can be created using the -a option of fftool. Detailed instructions on how to use fftool can be found here.
fftool 1 c4c1im.zmat 1 dca.zmat -b 20
packmol < pack.inp
fftool 1 c4c1im.zmat 1 dca.zmat -b 20 -a -l
polarizer -a alpha.ff data.lmp data-p.lmp
The polarizer script requires an input file (-f option) with parameters for Drude induced dipoles in the format:
# alpha.ff
type dm/u dq/e k/(kJ/molA2) alpha/A3 thole
CR 0.4 -1.0 4184.0 1.122 2.6
NA 0.4 -1.0 4184.0 1.208 2.6
...
dmis the mass to place on the Drude particle (taken from its core),dqis the charge of the Drude particle, the sign determines if the Drude particle is negative or positive; the value of dq may be computed from k and alpha,kis the harmonic force constant of the bond between core and Drude; the value of k may be computed from dq and alpha,alphais the polarizability of the atom,tholeis a parameter for the Thole damping function.
The force constant and the charge on the Drude particle are related though . Use the
-q option to read the force constant from alpha.ff and calculate Drude charges from the polarizabilities (default behavior), or else the -k option to read the Drude charge from alpha.ff and to calculate force constants from polarizabilities. The former is usually preferred.
A Drude particle is created for each atom found in the LAMMPS data data.lmp file that corresponds to an atom type given in the Drude file. Since LAMMPS uses numbers for atom types in the data file, the user needs to provide atom type names in comments after each line in the Masses section of the original LAMMPS data file, to allow identification of the atom types (fftool does this):
Masses
1 14.007 # NA
2 12.011 # CR
...
The polarizer script then adds new atom types, new bond types, new atoms and new bonds to a new data-p.lmp file. It also generates pair_coeff commands involving Drude particles that are written to a pair-drude.lmp file, which the user should include in the LAMMPS input script.
The polarizer script provides example commands to be included in the LAMMPS input script and writes those to in-drude.lmp. These commands are related to the topology and the force field, namely fix drude and pair_style commands, and include examples of thermostats:
# Commands to include in the LAMMPS input stack
# adapt the pair_style command as needed
pair_style hybrid/overlay ... coul/long/cs 12.0 thole 2.600 12.0
# new data file with Drude oscillators added
read_data data-p.lmp
# read pair interactions involving Drude particles
# Thole damping recommended if more than 1 Drude per molecule
include pair-drude.lmp
# convenient atom groups (for shake, thermostats...)
group ATOMS type 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
group CORES type 1 2 3 4 6 9 10 12 13 14 15
group DRUDES type 16 17 18 19 20 21 22 23 24 25 26
# identify each atom type: [C]ore, [D]rude, [N]on-polarizable
fix DRUDE all drude C C C C N C N N C C N C C C C D D D D D D D D D D D
# store velocity information of ghost atoms
comm_modify vel yes
variable TK equal 300.0
variable TDRUDE equal 1.0
variable PBAR equal 1.0
# temperature-grouped multiple Nose-Hoover thermostats and barostat
fix TSTAT all tgnpt/drude temp ${TK} ${TK} 100 ${TDRUDE} 20 iso ${PBAR} ${PBAR} 1000
# output the temperatures of molecular COM, COM of DC-DP, and DP
thermo_style custom step [...] f_TSTAT[1] f_TSTAT[2] f_TSTAT[3]
# write Drude particles to dump file
dump_modify ... element ... Dp Dp Dp Dp Dp Dp Dp Dp Dp Dp Dp
# ATTENTION!
# * read_data may need 'extra/special/per/atom' keyword, LAMMPS will exit with a message
# * if using fix shake the group-ID must not include Drude particles; use group ATOMS
# * give all I<=J pair interactions, no mixing
# * pair style coul/long/cs from CORESHELL package is used for interactions of DP;
# alternatively pair lj/cut/thole/long could be used avoiding hybrid/overlay and
# allowing mixing; see doc pages.
scaleLJ -f fragment.ff -a alpha.ff -i fragment.inp -ip pair.lmp -op pair-sc.lmp
The scaleLJ script scales LJ epsilon coefficients between fragments to prevent double counting of induction effects. This is needed if starting from a non-polarizable force field that implicitly includes polarization in the LJ terms. By default, the scaling factor is computed by this script from the charges and dipole moments of the fragments
Charges and dipole moments for new fragments can be calculated using quantum chemistry (we used the level MP2/cc-pVTZ). Details are given in the [CL&Pol] paper. Fragment charges and dipole moments are provided in the file fragment.ff:
# fragment.ff
MONOMERS
# name q/e mu/D
c2c1im 1.0 1.1558
...
DIMERS
# m1 m2 r_COM/A k_sapt
c2c1im dca 2.935 0.61
...
qis the charge of the monomer,muis the dipole moment of the monomer,m1andm2are the monomers forming a dimer,r_COMis the distance between the centers of mass of the monomers,k_saptis the scaling factor for the epsilon of LJ potential, obtained by SAPT quantum calculation (optional).
If equilibrium distances between centers of mass are missing for certain fragment dimers, these can be obtained from a geometry optimization (we used dispersion-corrected DFT, B97+D3/cc-pVTZ).
Values of the scaling factor can be obtained directly from quantum chemistry calculation, via Symmetry-Adapted Perturbation Theory (SAPT). If those are available in the fragment.ff file, they can be selected with the -q option.
In some cases it may be useful to scale sigma LJ values to adjust density, and this can be enabled with the -s option (which applies a default value of 0.985).
scaleLJ [...] -s - scale all fragments' sigma by 0.985
scaleLJ [...] -s 0.9 - scale all fragments' sigma by a user-defined value
scaleLJ [...] -s c2c1im c4h10 - scale the specified fragments' sigma by 0.985
scaleLJ [...] -s 0.9 c2c1im c4h10 - scale the specified fragments' sigma by a user-defined value
Finally, fragment.inp is a small input file that identifies the atomic types corresponding to each fragment, and should be prepared by the user for each system:
# fragment.inp
# c4c1im dca
c2c1im 1:8
C4H10 9:12
dca 13:15
where atomic indices or/and a range of indices correspond to atomic types associating with this fragment in the data.lmp. In this example, NA, CR, CW, C1, HCR, C1A, HCW, H1 belong to the c2c1im fragment; C2, CS, HC, CT are from the C4H10 fragment and N3A, CZA, NZA are from the dca fragment. Thus, the script requires c2c1im.zmat, C4H10.zmat and dca.zmat structure files for the fragments.
The scaleLJ script relies on several input files for fragment specification, fragment.ff, fragment.inp, molecular structure files of the fragments (in common formats .xyz, .zmat, .mol or .pdb) and on the pair.lmp file with the original pair coefficients of the non-polarizable system.
Scaled epsilon (and sigma) values for LJ interactions are written to a pair-sc.lmp file that can be included in the LAMMPS input script. The coefficients that were scaled are identified by a ~ character. The scaling coefficients used are also printed to the screen. If they are obtained by the prediction scheme, SAPT calculated values (if available) are shown only for the comparison.
Epsilon LJ coefficients were scaled by k_pred parameter. Changes are marked with '~'.
Sigma LJ coefficients were not scaled.
------------------------------------------
Fragment_i Fragment_j k_sapt k_pred
c2c1im c4h10 0.76 0.78
c2c1im dca 0.61 0.68
c4h10 c4h10 0.94 1.00
c4h10 dca 0.69 0.72
------------------------------------------
The CL&Pol force field can be mixed with other polarisable force fields, for example the SWM4-NDP model of water. In this case, the scaling of LJ epsilon should be performed only partially, and this can be controlled with -p option that identifies already polarisable fragments that don't need scaling:
python scaleLJ [...] -p swm4-ndp
The scaling coefficient will depend on the charge, dipole and molecular polarisability of this fragment only, the values of which should be specified in the input files for the scaleLJ script.
The scaling will only affect interactions with other fragments, the i-i Lennard-Jones coefficients involving this fragment will not be modified.
The input files of a system consisting of one ethylammonium nitrate ion pair can be found in the example_pil/ folder.
fftool 1 N2000.zmat 1 no3.zmat -b 20
packmol < pack.inp
fftool 1 N2000.zmat 1 no3.zmat -b 20 -a -l
polarizer -a alpha-pil.ff data.lmp data-p.lmp
scaleLJ -q -f fragment.ff -a alpha-pil.ff -i fragment.inp -ip pair.lmp -op pair-sc.lm
Here modification of the coefficients of LJ interactions between N2000 and NO3 fragments is performed using the scaling factor obtained through SAPT calculation (-q option).
Short-range damping is almost always needed between small, highly charged atoms (such as H) and induced dipoles to prevent the "polarization catastrophe".
coul_tt -d data-p.lmp -a 3
The functional form of the damping function is an adaptation of the Tang-Toennies damping function for dispersion interactions:
We set b = 4.5 and c = 1.0. This damping function is implemented in the coul/tt pair style in LAMMPS (version 29Oct20 or newer) with details given here.
The coul_tt script requires the data-p.lmp file to obtain the list of atoms and their type (polarisable or non-polarisable).
1 13.607 # N1 DC
2 11.611 # C1N DC
3 1.008 # HN
4 11.611 # CEN DC
5 1.008 # H1N
6 1.008 # HCN
7 13.601 # NO DC
8 15.599 # ON DC
9 0.400 # N1 DP
10 0.400 # C1N DP
11 0.400 # CEN DP
12 0.400 # NO DP
13 0.400 # ON DP
The atomic indices of small, highly charged atoms (typically, point charges without LJ sites) should be specified with the -a option and sepatared with spaces. The short-range Coulomb interactions of those atoms with all Drude cores and Drude particles will be damped. The corresponding pair_coeff lines are written to a pair-tt.lmp file.
pair_coeff 1 3 coul/tt 4.5 1.0
pair_coeff 2 3 coul/tt 4.5 1.0
pair_coeff 3 4 coul/tt 4.5 1.0
pair_coeff 3 7 coul/tt 4.5 1.0
pair_coeff 3 8 coul/tt 4.5 1.0
pair_coeff 3 9* coul/tt 4.5 1.0
In this example, the damped interactions are the ones of the HN atom (index 3) with Drude cores (indices 1, 2, 4, 7, 8) and Drude particles (indices 9-13).
The coul_tt script prints the commands to be included by the user to the in-p.lmp file to declare the coul/tt pair style.
To include in in-p.lmp:
pair_style hybrid/overlay ... coul/tt 4 12.0
include pair-tt.lmp
Hydrogen bonds (D-H...A) involving hydrogen atoms represented by 'naked' charges without Lennard-Jones sites can lead to "freezing" of a system when modelled using a polarisable force field. To avoid this, the repulsive potential between D and A sites can be adjusted, with a typical value of the sigma coefficient of 3.7 to 3.8 Å.
In EAN, the hydrogen bond is formed between HN atoms of the cation embedded into neighbouring N1 atoms and the ON atoms of the anion. The LJ sigma coefficient of the N1-ON interaction should be increased from 3.10 Å to 3.75 Å.
The pair_coeff coefficients of the interaction between N1 and ON atoms in the pair-sc.lmp file
pair_coeff 1 8 lj/cut/coul/long 0.037789 3.101612 # N1 ON
should be replaced by
pair_coeff 1 8 lj/cut/coul/long 0.037789 3.750000 # N1 ON
-
Packmol: L. Martinez et al. J Comp Chem 30 (2009) 2157, DOI: 10.1002/jcc.21224
-
LAMMPS: S. Plimton, J Comp Phys 117 (1995) 1, DOI: 10.1006/jcph.1995.1039
-
CL&Pol: K. Goloviznina, J. N. Canongia Lopes, M. Costa Gomes, A. A. H. Pádua, J. Chem. Theory Comput. 15 (2019), 5858, DOI: 10.1021/acs.jctc.9b00689, arXiv 1703.01540
-
CL&Pol for PIL, DES, electrolytes: K. Goloviznina, Z. Gong, M. Costa Gomes, A. A. H. Pádua, J. Chem. Theory Comput. (2021) DOI: 10.26434/10.1021/acs.jctc.0c01002, ChemRxiv 10.26434/chemrxiv.12999524