A Swiss army knife to generate proton-disordered ice structures.
- Python 3
- NetworkX
- numpy
Note: WinPython includes all of these requirements.
GenIce is registered to PyPI (Python Package Index). Install with pip3.
pip3 install genice
pip3 uninstall genice
usage: genice [-h] [--rep REP REP REP] [--dens DENS] [--seed SEED]
[--format gmeqdypoc] [--water model] [--guest D=empty]
[--Guest 13=me] [--Group 13=bu-:0] [--anion 3=Cl]
[--cation 3=Na] [--nodep] [--debug] [--quiet]
Type
positional arguments:
Type Crystal type (1c,1h,etc. See
https://github.com/vitroid/GenIce for available ice
structures.)
optional arguments:
-h, --help show this help message and exit
--rep REP REP REP, -r REP REP REP
Repeat the unit cell in x,y, and z directions. [2,2,2]
--dens DENS, -d DENS Specify the ice density in g/cm3
--seed SEED, -s SEED Random seed [1000]
--format gmeqdypoc, -f gmeqdypoc
Specify file format [g(romacs)|m(dview)|e(uler)|q(uate
rnion)|d(igraph)|y(aplot)|p(ython
module)|o(penScad)|c(entersofmass)|r(elative com)]
--water model, -w model
Specify water model. (tip3p, tip4p, etc.)
--guest D=empty, -g D=empty
Specify guest(s) in the cage type. (D=empty,
T=co2*0.5+me*0.3, etc.)
--Guest 13=me, -G 13=me
Specify guest in the specific cage. (13=me, 32=co2,
etc.)
--Group 13=bu-:0, -H 13=bu-:0
Specify the group. (-H 13=bu-:0, etc.)
--anion 3=Cl, -a 3=Cl
Specify a monatomic anion that replaces a water
molecule. (3=Cl, 39=F, etc.)
--cation 3=Na, -c 3=Na
Specify a monatomic cation that replaces a water
molecule. (3=Na, 39=NH4, etc.)
--nodep No depolarization.
--debug, -D Output debugging info.
--quiet, -q Do not output progress messages.
Use ./genice.x instead of genice if you want to use GenIce without installation.
-
To make a 3x3x3 units of a hydrogen-disordered ice IV (4) of TIP4P water in GROMACS .gro format:
genice --water tip4p --rep 3 3 3 4 > ice4.gro -
To make a 2x2x4 units of CS2 clathrate hydrate structure of TIP4P water containing THF (united atom with a dummy site) in the large cage in GROMACS .gro format:
genice -g 16=uathf6 --water tip4p --rep 2 2 4 CS2 > cs2-224.gro
The program generates various ice lattice with proton disorder and without defect. Total dipole moment is always set to zero (except the case you specify --nodep option). The minimal structure (with --rep 1 1 1 option) is not always the unit cell of the lattice because it is difficult to deal with the hydrogen bond network topology of tiny lattice under periodic boundary condition. Note that the generated structure is not optimal according to the potential energy.
-
To get a large repetition of ice Ih in XYZ format,
genice --rep 8 8 8 1h --format xyz > 1hx888.xyz -
To get a ice V lattice of different hydrogen order in CIF format, use
-soption to specify the random seed.genice 5 -s 1024 --format cif > 5-1024.cif -
To obtain a ice VI lattice with different density and with TIP4P water model in gromacs format, use
--dens xoption to specify the density in g cm-3.genice 6 --dens 1.00 --format g --water tip4p > 6d1.00.gro
For clathrate hydrates, you can prepare the lattice with cages partially occupied by various guest molecules.
-
To make a CS1 clathrate hydrate structure of TIP4P water containing CO2 in GROMACS .gro format: (60% of small cages are filled with co2 and 40% are methane)
genice -g 12=co2*0.6+me*0.4 -g 14=co2 --water tip4p CS1 > cs1.gro -
To make a CS2 clathrate hydrate structure of TIP5P water containing THF molecules in the large cage, while only one cage is filled with methane molecule, first just run genice without guest specifications:
genice CS2 > CS2.groThe list of cages will be output as follows:
INFO Cage types: ['12', '16'] INFO Cage type 12: {0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183} INFO Cage type 16: {136, 137, 138, 139, 140, 141, 142, 143, 16, 17, 18, 19, 20, 21, 22, 23, 160, 161, 162, 163, 164, 165, 166, 167, 40, 41, 42, 43, 44, 45, 46, 47, 184, 185, 186, 187, 188, 189, 190, 191, 64, 65, 66, 67, 68, 69, 70, 71, 88, 89, 90, 91, 92, 93, 94, 95, 112, 113, 114, 115, 116, 117, 118, 119}This indicates that there are two types of cages named
12and16. Fill the16cages with THF and put a methane molecule in the0th cage of type12as follows:genice CS2 -g 16=uathf -G 0=me > CS2.gro
Although only a few kinds of guest molecules are preset, you can easily prepare new guest molecules as a module. Here is an example for the ethlene oxide molecule.
eo.py
import numpy as np
# United-atom EO model with a dummy site
LOC = 0.1436 # nm
LCC = 0.1472 # nm
Y = (LOC**2 - (LCC/2)**2)**0.5
sites = np.array([[ 0., 0., 0. ],
[-LCC/2, Y, 0. ],
[+LCC/2, Y, 0. ],])
mass = np.array([16,14,14])
# center of mass
CoM = np.dot(mass, sites) / np.sum(mass)
sites -= CoM
atoms = ["O","C","C"]
labels = ["Oe","Ce","Ce"]
name = "EO"
Write the code in eo.py and put it in the user module folder at either
| OS | folder path |
|---|---|
| Linux | ~/.github/GenIce/molecules |
| MacOS | ~/Library/Application Support/GenIce/molecules |
Note: multiple occupancy is not implemented. If it is required, make a module of a virtual molecule that contains multiple molecules.
The structure of aeroice[Matsui 2017] is built of polyhedra and polygonal prisms that are the nodes and edges of the super-network. If the length of the prisms is extended, the structure becomes very sparse.
The aeroice nxFAU is an extended structure derived from a zeolitic ice FAU by stretching the hexagonal prisms n-tuply. The super-network of nxFAU is isomorphic to diamond (i.e., ice 1c) and therefore the nxFAU structure can be made from ice 1c using Utilities/decorator.py utility.
First, prepare a unit cell of ice 1c in AR3R format (AR3R is a file format containing the cell dimensions and the fractional coordinates of the center of mass of the water molecules).
% genice 1c -r 1 1 1 --format r > 1c.ar3r
Then decorator.py reads it and regards it as the topology of the super-network, and decorate (put water molecules appropriately) to make nxFAU. The command generates the lattice module for genice to make 4xFAU as an example.
% Utilities/decorator.py 4 < 1c.ar3r > 4xFAU.py
Put 4xFAU.py module in the user's lattice module folder at either
| OS | folder path |
|---|---|
| Linux | ~/.github/GenIce/lattices |
| MacOS | ~/Library/Application Support/GenIce/lattices |
and make 4xFAU structure by GenIce.
% genice 4xFAU > 4xFAU.gro
Note that decorator.py is applicable only to ice 1c structure for now. Other ice structures are somewhat distorted and therefore not suitable for decoration.
Small ions may replace the host molecules. In that case, you can use -a and -c options to replace the specified water molecules with anions and cations.
The following example replaces the 0th water molecule (in the replicated lattice) with Na cation and 1st water molecule with Cl anion. The hydrogen bonds around the ions are organized appropriately.
genice CS2 --nodep -c 0=Na -a 1=Cl > CS2.gro
Note 1: The numbers of cations and anions must be the same. Otherwise, ice rule is never satisfied and the program does not stop.
Note 2: The option --nodep is also required because it is impossible to depolarize the structure containing ions.
Note 3: Protonic defects (H3O+ and OH-) are not yet implemented.
Let us assume that the id of the water molecule to be replaced by nitrogen of the TBA as zero. Place the nitrogen as a cation and also replace the water 2 by the counterion Br.
genice HS1 -c 0=N -a 2=Br --nodep > HS1.gro
Then you will see the following info.
INFO Hints:
INFO Cage types: ['12', '14', '15']
INFO Cage type 12: {0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 56, 57, 58, 59, 60, 61, 70, 71, 72, 73, 74, 75, 84, 85, 86, 87, 88, 89, 98, 99, 100, 101, 102, 103}
INFO Cage type 14: {6, 7, 8, 9, 20, 21, 22, 23, 34, 35, 36, 37, 48, 49, 50, 51, 62, 63, 64, 65, 76, 77, 78, 79, 90, 91, 92, 93, 104, 105, 106, 107}
INFO Cage type 15: {10, 11, 12, 13, 24, 25, 26, 27, 38, 39, 40, 41, 52, 53, 54, 55, 66, 67, 68, 69, 80, 81, 82, 83, 94, 95, 96, 97, 108, 109, 110, 111}
INFO Cages adjacent to dopant 2: {9, 2, 28, 97}
INFO Cages adjacent to dopant 0: {9, 2, 28, 7}
It indicates that the nitrogen is surrounded by cages with ids 9, 2, 28, and 7. Types for these cages can also be found in the info. Then, we put the Bu- group (minus does not mean ions) in these cages adjacent dopant 0.
genice HS1 -c 0=N -a 2=Br -H 9=Bu-:0 -H 2=Bu-:0 -H 28=Bu-:0 -H 7=Bu-:0 --nodep > HS1.gro
Here the option -H specifies the group by -H (cage id)=(group name):(root), and root is the nitrogen that is specified by -c (cation) option.
Under preparation
It is more convenient if the lattice of the semiclathrate hydrate contains molecular ions in the appropriate locations in advance. Here we explain the way to make the special module for semclathrates.
| Name | Application | extension | water | solute | HB | remarks |
|---|---|---|---|---|---|---|
cif |
CIF | .cif |
Atomic positions | Atomic positions | none | Experimental |
g, gromacs |
Gromacs | .gro |
Atomic positions | Atomic positions | none | |
m, mdview |
MDView | .mdv |
Atomic positions | Atomic positions | auto | |
o, openscad |
OpenSCAD | .scad |
Center of mass | none | o | |
povray |
Povray module | .pov |
Atomic positions | Atomic Positions | o | |
towhee |
TowHee | .coords(?) |
Atomic positions | Atomic positions | none | |
xyz |
XYZ | .xyz |
Atomic positions | Atomic positions | none | Experimental |
y, yaplot |
Yaplot | .yap |
Atomic positions | Atomic positions | o | |
e, euler |
Euler angles | .nx3a |
Rigid rotor | none | none | |
q, quaternion |
Quaternions | .nx4a |
Rigid rotor | none | none | |
d, digraph |
Digraph | .ngph |
none | none | o | |
graph |
Graph | .ngph |
none | none | o | Experimental. |
c, com |
CenterOfMass | .ar3a |
Center of mass | none | none | |
r, rcom |
Relative CoM | .ar3r |
Center of mass | none | none | In fractional coordinate system. |
p, python |
Python module | .py |
Center of mass | none | none | Under development. |
| Symbol | Description |
|---|---|
| 1h, 1c | Most popular Ice I (hexagonal or cubic) |
| 2 | Proton-ordered ice II |
| 2d | Hypothetical Proton-disordered Ice II.[Nakamura 2015] |
| 3, 4, 6, 7, 12 | Conventional high-pressure ices III, IV, VI, VII, and XII.[Lobban 1998] |
| 5 | Monoclinic ice V (testing). |
| 16 | Negative-pressure ice XVI(16).[Falenty 2014] |
| 17 | Negative-pressure ice XVII(17).[del Rosso 2016] |
| 0 | Hypothetical ice "0".[Russo 2014] |
| i | Hypothetical ice "i". = Zeolite BCT.[Fennell 2005] |
| C0, C0-II | Filled ice C0 (Alias of 17).[Smirnov 2013] |
| C1 | Filled ice C1 (Alias of 2).[Londono 1988] |
| C2 | Filled ice C2 (Alias of 1c).[Vos 1993] |
| sTprime | Filled ice "sT'" [Smirnov 2013] |
| CS1, CS2, CS4, TS1, HS1, HS2, HS3 | Clathrate hydrates, Kosyakov's nomenclature. [Kosyakov 1999] |
| sI, sII, sIII, sIV, sV, sVII, sH | Clathrate hydrates, Jeffrey's nomenclature. Jeffrey 1984] |
| RHO | Hypothetical ice at negative pressure ice "sIII".[Huang 2016] |
| FAU | Hypothetical ice at negative pressure ice "sIV". [Huang 2017] |
| CRN1, CRN2, CRN3 | 4-coordinated continuous random network [Mousseau 2005] |
| Struct01 .. Struct84 | Space Fullerenes [Dutour Sikiric 2010] |
| A15, sigma, Hcomp, Z, mu, zra-d, 9layers, 6layers, C36, C15, C14, delta, psigma | Space Fullerenes, Aliases of the Struct?? series. See the data source for their names. [Dutour Sikiric 2010] |
| T | Space fullerene type T,[Dutour Sikiric 2010] II+IVa. [Karttunen 2011] |
| 2xFAU, 4xFAU, 8xFAU, 16xFAU, 32xFAU, 64xFAU | Aeroices.[Matsui 2017] |
| iceR | Partial plastic ice R [Mochizuki 2014]. |
| iceT | Partial plastic ice T [Hirata 2017]. |
Ice names with double quotations are not experimentally verified.
Note: Some structures in different frameworks are identical.
| CH/FI | CH | ice | FK | Zeo |
|---|---|---|---|---|
| sI | CS1 | - | A15 | MEP |
| sII | CS2 | 16 | C15 | MTN |
| sIII | TS1 | - | sigma | - |
| sIV | HS1 | - | Z | - |
| sV | HS2 | - | * | - |
| sVII | CS4 | - | * | SOD |
| sH | HS3 | - | * | DOH |
| C0 | - | 17 | * | - |
| C1 | - | 2 | * | - |
| C2 | - | 1c | * | - |
FI: Filled ices; CH: Clathrate hydrates; FK:Frank-Kasper duals; Zeo: Zeolites.
-: No correspondence; *: Non-FK types; @: Not included in GenIce.
Please ask [email protected] to add new ice structures.
A water model can be chosen with --water option.
| symbol | type |
|---|---|
3site, tip3p |
3-site TIP3P (default) |
4site, tip4p |
4-site TIP4P |
ice |
TIP4P/ice |
5site, tip5p |
5-site TIP5P |
6site, NvdE |
6-site NvdE |
| symbol | type |
|---|---|
co2 |
CO2 |
me |
United atom monatomic methane |
uathf |
United atom 5-site THF |
g12,g14,g15,g16 |
A monatomic dummy site |
empty |
Leave the cage empty. |
- L. del Rosso, M. Celli, L. Ulivi, Nat Commun 2016, 7, 13394. DOI: 10.1038/ncomms13394
- M. Dutour Sikirić, O. Delgado-Friedrichs, M. Deza, Acta Crystallogr. A 2010, 66, 602. DOI: 10.1107/S0108767310022932
- A. Falenty, T. C. Hansen, W. F. Kuhs, Nature 2014, 516, 231. DOI: 10.1038/nature14014
- C. J. Fennell, J. D. Gezelter, J. Chem. Theory Comput. 2005, 1, 662. DOI: 10.1021/ct050005s
- M. Hirata, T. Yagasaki, M. Matsumoto, H. Tanaka, to be published in Langmuir (2017). DOI: 10.1021/acs.langmuir.7b01764
- Y. Huang, C. Zhu, L. Wang, X. Cao, Y. Su, X. Jiang, S. Meng, J. Zhao, X. C. Zeng, Science Advances 2016, 2, e1501010. DOI: 10.1126/sciadv.1501010
- Y. Huang, C. Zhu, L. Wang, J. Zhao, X. C. Zeng, Chem. Phys. Lett. 2017, 671, 186. DOI: 10.1016/j.cplett.2017.01.035
- G. A. Jeffrey, In Inclusion Compounds; J. L. Atwood, J. E. D. Davies, D. D. MacNicol, Eds.; Academic Press: London, 1984, Vol. 1, Chap. 5.
- A. J. Karttunen, T. F. Fässler, M. Linnolahti, T. A. Pakkanen, Inorg Chem 2011, 50, 1733. DOI: 10.1021/ic102178d
- V. I. Kosyakov, T. M. Polyanskaya, J. Struct. Chem. 1999, 40, 239. DOI: 10.1007/BF02903652
- D. Londono, W. F. Kuhs, J. L. Finney, Nature 1988, 332, 141. DOI: 10.1038/332141a0
- T. Matsui, M. Hirata, T. Yagasaki, M. Matsumoto, H. Tanaka, J. Chem. Phys. 147, 091101 (2017). DOI: /10.1063/1.4994757
- K. Mochizuki, K. Himoto, and M. Matsumoto, Phys. Chem. Chem. Phys. 16, 16419–16425 (2014). DOI: 10.1039/c4cp01616e
- N. Mousseau, G. T. Barkema, Curr. Opin. Solid State Mater. Sci. 2001, 5, 497. DOI: 10.1016/S1359-0286(02)00005-0
- T. Nakamura, M. Matsumoto, T. Yagasaki, H. Tanaka, J. Phys. Chem. B 2015, 120, 1843. DOI: 10.1021/acs.jpcb.5b09544
- C. Lobban, J. L. Finney, W. F. Kuhs, Nature 1998, 391, 268. DOI: 10.1038/34622
- J. Russo, F. Romano, H. Tanaka, Nat Mater 2014, 13, 733. DOI: 10.1038/NMAT3977
- G. S. Smirnov, V. V. Stegailov, J Phys Chem Lett 2013, 4, 3560. DOI: 10.1021/jz401669d
- W. L. Vos, L. W. Finger, R. J. Hemley, H. Mao, Phys. Rev. Lett. 1993, 71, 3150. DOI: 10.1103/PhysRevLett.71.3150
M. Masakazu, T. Yagasaki, and H. Tanaka,"GenIce: Hydrogen-DIsordered Ice Generator", J. Comput. Chem. 39, 61-64 (2017). DOI: 10.1002/jcc.25077
GenIce is served at the GitHub (https://github.com/vitroid/GenIce) as an open source software since 2015. Feedbacks, proposals for improvements and extensions, and bug fixes are sincerely appreciated. Developers and test users are also welcome.