GenIce2

A Swiss army knife to generate hydrogen-disordered ice structures.

Version 2.2.12.3

New in GenIce2.2

• The core algorithm and its API are in a separate module, genice-core.

Demo

The new GenIce works very well with interactive execution. Try instantly on Google Colaboratory.

Requirements

• networkx>=2.0.dev20160901144005
• python^3.10
• numpy^2.0
• pairlist>=0.6
• cycless>=0.4.2
• graphstat>=0.3.3
• yaplotlib>=0.1.2
• openpyscad>=0.5.0
• genice-core>=1.1
• deprecation^2.1.0

Installation

GenIce is registered to PyPI (Python Package Index). Install with pip3.

shell % pip3 install genice2

Uninstallation

shell % pip3 uninstall genice2

Usage

usage: genice2 [-h] [--version] [--rep REP REP REP] [--reshape RESHAPE]
               [--shift SHIFT SHIFT SHIFT] [--dens DENS] [--add_noise percent]
               [--seed SEED] [--format name] [--water model] [--guest 14=me]
               [--Guest 13=me] [--Group 13=bu-:0] [--anion 3=Cl]
               [--cation 3=Na] [--depol DEPOL] [--asis] [--debug] [--quiet]
               [--assess_cages]
               Type

GenIce is a swiss army knife to generate hydrogen-disordered ice structures.
(version 2.2.12.3)

positional arguments:
  Type                  Crystal type (1c, 1h, etc. See
                        https://github.com/vitroid/GenIce for available ice
                        structures.)
                        If you want to analyze your own structures, please try
                        analice tool.


                        [Available lattice structures]

                        1. Lattice structures served with GenIce

                        0, ice0         Metastable ice "0".
                        11, XI, ice11   A candidate for an antiferroelectric
                                        Ice XI #19.
                        115_2_114, 12_1_11, 144_2_7301, 151_2_4949650,
                                        153_2_155471, 176_2_5256, 207_1_4435,
                                        2_2_623457, ACO, CS4, DDR, IWV, LTA,
                                        MAR, NON, PCOD8007225, PCOD8036144,
                                        PCOD8204698, PCOD8301974, PCOD8321499,
                                        PCOD8324623, SGT, SOD, engel01,
                                        engel03, engel04, engel17, engel20,
                                        engel23, engel24, engel26, engel29,
                                        engel30, engel31, engel34, sVII
                                        Hypothetical zeolitic ice
                        11alt           A layered ferroelectric Ice XI.
                        11i             Sixteen candidates for Ice XI.
                        12, XII, ice12  Metastable high-pressure ice XII.
                        13, XIII, ice13 Ice XIII, a hydrogen-ordered
                                        counterpart of ice V.
                        14, ice14       Ice XIV, a partially hydrogen-ordered
                                        counterpart of ice XII. Note that it
                                        does not reproduce the occupancies
                                        (probability of occupation) of the
                                        possible hydrogen sites.
                        16, CS2, MTN, XVI, ice16, sII   Ultralow-density Ice
                                        XVI.
                        17, XVII, ice17 Ultralow-density Ice XVII.
                        1c, Ic, ice1c   Cubic type of ice I.
                        1h, Ih, ice1h   Most popular Ice I (hexagonal). NOTE:
                                        Due to a historical reason, the crystal
                                         axes of hexagonal ice are exchanged.
                                        If you want the basal plane to be Z
                                        axis, please use 'one[hh]' instead.
                        2, II, ice2     Hydrogen-ordered ice II.
                        2D3             Trilayer honeycomb ice.
                        2d, ice2d, ice2rect             A hydrogen-disordered
                                        counterpart of ice II.
                        3, III, ice3    Ice III.
                        4, IV, ice4     Ice IV.
                        4R              Orthogonalized ice IV.
                        5, V, ice5      Monoclinic ice V (testing).
                        5R              Ice V with orthogonal unit cell.
                                        (testing)
                        6, VI, ice6     Conventional high-pressure ice VI.
                        6h              Half lattice of ice VI.
                        7, VII, ice7    Conventional high-pressure ice VII.
                        8, VIII, ice8   Ice VIII, a hydrogen-ordered
                                        counterpart of ice VII.
                        9, IX, ice9     Ice IX, a hydrogen-ordered counterpart
                                        of ice III.
                        A, iceA         Hypothetical ice A.
                        A15, Struct33   Cubic Structure I of clathrate hydrate.
                        B, iceB         Hypothetical ice B.
                        BSV, engel05    Hypothetical zeolitic ice of the gyroid
                                         structure.
                        C14, C15, C36, FK6layers, FK9layers, HS2, Hcomp,
                                        Struct01, Struct03, Struct04, Struct05,
                                         Struct06, Struct07, Struct08,
                                        Struct09, Struct10, Struct11, Struct12,
                                         Struct13, Struct14, Struct15,
                                        Struct16, Struct17, Struct18, Struct19,
                                         Struct20, Struct21, Struct22,
                                        Struct23, Struct24, Struct25, Struct26,
                                         Struct27, Struct28, Struct29,
                                        Struct30, Struct31, Struct32, Struct34,
                                         Struct35, Struct36, Struct37,
                                        Struct38, Struct39, Struct40, Struct41,
                                         Struct42, Struct43, Struct44,
                                        Struct45, Struct46, Struct47, Struct48,
                                         Struct49, Struct50, Struct51,
                                        Struct52, Struct53, Struct54, Struct55,
                                         Struct56, Struct57, Struct58,
                                        Struct59, Struct60, Struct61, Struct62,
                                         Struct63, Struct64, Struct65,
                                        Struct66, Struct67, Struct68, Struct69,
                                         Struct70, Struct71, Struct72,
                                        Struct73, Struct74, Struct75, Struct76,
                                         Struct77, Struct78, Struct79,
                                        Struct80, Struct81, Struct82, Struct83,
                                         Struct84, Z, delta, mu, psigma, sV,
                                        sigma, zra-d     A space fullerene.
                        CRN1, CRN2, CRN3                A continuous random
                                        network of Sillium.
                        CS1, MEP, sI    Clathrate hydrates sI.
                        DOH, HS3, sH    Clathrate type H.
                        EMT             Hypothetical ice with a large cavity.
                        FAU             Hypothetical ice at negative pressure
                                        ice 'sIV'.
                        HS1, sIV        Hydrogen-disordered ice Ih.
                        M, iceM         A hypothetical hydrogen-ordered high-
                                        density ice.
                        RHO             Hypothetical ice at negative pressure
                                        ice 'sIII'.
                        Struct02        A space fullerene. (I phase?)
                        T               Hypothetical clathrate type T.
                        XIc-a           A candidate for the proton-ordered
                                        counterpart of ice Ic. The structure
                                        'a' in Figure 1.
                        YKD             Ice in a d-surface (testing).
                        bilayer         A Bilayer Honeycomb Ice Phase in
                                        Hydrophobic Nanopores.
                        c0te            Filled ice C0 by Teeratchanan
                                        (Hydrogen-disordered.) (Positions of
                                        guests are supplied.)
                        c1te            Hydrogen-ordered hydrogen hydrate C1 by
                                         Teeratchanan. (Positions of guests are
                                         supplied.)
                        c2te            Filled ice C2 (cubic ice) by
                                        Teeratchanan (Hydrogen disordered).
                                        (Positions of guests are supplied.)
                        eleven          Ice XI w/ stacking faults.
                        i               Hypothetical ice "i".
                        ice1hte         Filled ice Ih by Teeratchanan (Hydrogen
                                         disordered). (Positions of guests are
                                        supplied.)
                        iceL            The hypothetical Ice L
                        iceMd           A hydrogen-disordered counterpart of
                                        ice M.
                        iceR            Hypothetical ice R.
                        iceT            Hypothetical ice T.
                        iceT2           Hypothetical ice T2.
                        one             Ice I w/ stacking disorder.
                        oprism          Hydrogen-ordered ice nanotubes.
                        sTprime         Filled ice sT'.
                        xFAU            Aeroice xFAU.
                        xdtc            A porous ice with cylindrical channels.
                        ----
                        (Undocumented) 1h_unit TS1 dtc ice1h_unit sIII


                        2. Lattice structures served by external plugins

                        cif             Read a CIF file.
                        ----
                        (Undocumented) zeolite


                        3. Lattice structures served locally

                        (None)
                        ----



options:
  -h, --help            show this help message and exit
  --version, -V         show program's version number and exit
  --rep REP REP REP, -r REP REP REP
                        Repeat the unit cell along a, b, and c axes. [1,1,1]
  --reshape RESHAPE, -R RESHAPE
                        Convert the unit cell shape by specifying the new
                        (a,b,c) set from the original (a,b,c) of the unit
                        cell. The combination of (a,b,c) is specified by nine
                        integers. For example, '--reshape 3,0,0,0,2,0,0,0,1'
                        specifies that the new cell vectors are (3a, 2b, c),
                        which is equivalent to '--rep 3 2 1'.
  --shift SHIFT SHIFT SHIFT, -S SHIFT SHIFT SHIFT
                        Shift the unit cell along a, b, and c axes. (0.5==half
                        cell) [0,0,0]
  --dens DENS, -d DENS  Specify the ice density in g/cm3 (Guests are not
                        included.)
  --add_noise percent   Add a Gauss noise with given width (SD) to the
                        molecular positions of water. The value 1 corresponds
                        to 1 percent of the molecular diameter of water.
  --seed SEED, -s SEED  Random seed [1000]
  --format name, -f name
                        Specify the output file format. [gromacs]


                        [Available formatters]

                        1. Formatters served with GenIce

                        _KG             Kirkworrd G factor.
                        _ringstat       Bond direction statistics.
                        d, digraph      Directed graph of HBs.
                        e, euler        Rigid rotor (Euler angle).
                        exmol           Extended XMol file format.
                        exyz            Extended XYZ format.
                        g, gromacs      Gromacs .gro file.
                        graph           Undirected graph of HBs.
                        m, mdview       MDView file (in Angdtrom).
                        mdv_au          MDView file (in au).
                        p, python       A formatter plugin to produce a python
                                        lattice plugin.
                        povray          Povray.
                        q, quaternion   Rigid rotor (Quaternion).
                        raw             Raw data. (For use with Jupyter)
                        rings           Show rings in Yaplot.
                        y, yaplot       Yaplot.
                        ----
                        (Undocumented) c cif cif2 com null r rcom towhee xyz


                        2. Formatters served by external plugins

                        cage            Cage analysis.
                        mdanalysis      MDAnalysis integration.
                        png             PNG (Portable Network Graphics).
                        svg             SVG (Standard Vector Graphics).
                        ----


                        3. Formatters served locally

                        (None)
                        ----


  --water model, -w model
                        Specify the water model. [tip3p]


                        [Available molecules]

                        1. Molecules served with GenIce

                        3site, tip3p    A typical 3-site model.
                        4site, tip4p    A typical 4-site model.
                        5site, tip5p    A typical 5-site model.
                        6site, NvdE     A 6-site water model.
                        7site           A seven-site water model.
                        physical_water  Physical model of water; Oxygen atom is
                                         on the lattice point.
                        ----
                        (Undocumented) ice spce


                        2. Molecules served by external plugins

                        (None)
                        ----


                        3. Molecules served locally

                        (None)
                        ----


  --guest 14=me, -g 14=me
                        Specify guest(s) in the cage type. (D=empty,
                        T=co2*0.5+me*0.3, etc.)


                        [Available molecules]

                        1. Molecules served with GenIce

                        H2              Hydrogen molecule.
                        ch4             An all-atom methane model.
                        et              A united-atom ethane model.
                        me              A united-atom methane model.
                        mol             Loader for MOL files (generated by
                                        MolView.org), e.g. mol[THF.mol].
                        thf             An all-atom tetrahydrofuran (THF)
                                        model.
                        uathf           A united-atom five-site tetrahydrofuran
                                         (THF) model.
                        ----
                        (Undocumented) co2 empty g12 g14 g15 g16 one uathf6


                        2. Molecules served by external plugins

                        (None)
                        ----


                        3. Molecules served locally

                        (None)
                        ----


  --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.)
  --depol DEPOL         Depolarization. (strict, optimal, or none) ["strict"]
  --asis                Assumes all given HB pairs to be fixed. No shuffle and
                        no depolarization.
  --debug, -D           Output debugging info.
  --quiet, -q           Do not output progress messages.
  --assess_cages, -A    Assess the locations of cages based on the HB network
                        topology. Note: it may fail when the unit cell is too
                        small.

Use ./genice.x instead of genice2 if you want to use it inside the source tree.

Examples

• To make a 3x3x3 units of a hydrogen-disordered ice IV (4) of TIP4P water in GROMACS .gro format:

genice2 --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:

genice2 -g 16=uathf6 --water tip4p --rep 2 2 4 CS2 > cs2-224.gro

Basics

The program generates various ice lattice with proton disorder and without defect. The total dipole moment is always set to zero (except in the case you specify --depol 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,

  genice2 --rep 8 8 8 1h --format xyz > 1hx888.xyz
  

• To get a ice V lattice of different hydrogen order in CIF format, use -s option to specify the random seed.

  genice2 5 -s 1024 --format cif > 5-1024.cif
  

• To obtain an ice VI lattice with different density and with TIP4P water model in gromacs format, use --dens x option to specify the density in g cm^-3.

  genice2 6 --dens 1.00 --format g --water tip4p > 6d1.00.gro
  

GenIce is a modular program; it reads a unit cell data from a lattice plugin defined in the lattices folder, put water and guest molecules using a molecule plugin defined in the molecules/ folder, and output in various formats using a format plugin defined in the formats/ folder. You can write your plugins to extend GenIce. Some plugins also accept options.

Clathrate hydrates

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)

  genice2 -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 genice2 without guest specifications:

  genice2 CS2 > CS2.gro
  

The 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 12 and 16. Fill the 16 cages with THF and put a methane molecule in the 0th cage of type 12 as follows:

    genice2 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 of the ethylene oxide molecule.

```python import numpy as np import genice2.molecules

class Molecule(genice2.molecules.Molecule): def init(self): # United-atom EO model with a dummy site LOC = 0.1436 # nm LCC = 0.1472 # nm

    Y = (LOC**2 - (LCC/2)**2)**0.5

    self.sites = np.array([[ 0.,    0., 0. ],
                           [-LCC/2, Y,  0. ],
                           [+LCC/2, Y,  0. ],])

    mass = np.array([16,14,14])
    # center of mass
    CoM = mass @ self.sites / np.sum(mass)
    self.sites -= CoM

    self.atoms_  = ["O","C","C"]
    self.labels_ = ["Oe","Ce","Ce"]
    self.name_   = "EO"

```

Write the code in eo.py. Make a folder named molecules in the current working directory and put it in.

Note: multiple occupancy is not implemented. If it is required, make a module of a virtual molecule that contains multiple molecules.

Doping ions

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.

genice2 CS2 --depol=optimal -c 0=Na -a 1=Cl > CS2.gro

Note 1: The numbers of cations and anions must be the same. Otherwise, the ice rule is never satisfied and the program does not stop.

Note 2: The option --depol=optimal is also required because it is impossible to completely depolarize the structure containing ions.

Note 3: Protonic defects (H₃O⁺ and OH^-) are not yet implemented.

Semiclathrate hydrates

Placement of a tetrabutylammonium ion (testing)

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 counter-ion Br.

genice2 HS1 -c 0=N -a 2=Br --depol=optimal > 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} INFO Cage type 14: {8, 9, 6, 7} INFO Cage type 15: {10, 11, 12, 13} ... INFO Stage7: Arrange guest atoms. INFO Cages adjacent to dopant 2: {0, 9, 2, 13} INFO Cages adjacent to dopant 0: {0, 9, 2, 7}

It indicates that the nitrogen is surrounded by cages with ids 0, 9, 2, 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 to dopant 0.

shell % genice2 HS1 -c 0=N -a 2=Br -H 0=Bu-:0 -H 9=Bu-:0 -H 2=Bu-:0 -H 7=Bu-:0 --depol=optimal > HS1.gro

Here the option -H specifies the group by -H (cage id)=(group name):(root), and the root is the nitrogen that is specified by -c (cation) option.

Placement of TBAB in the lattice module

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.

Output formats

| Name | Application | extension | water | solute | HB | remarks | | ------------------------ | --------------------------------------------------------------------------------------------------------------------- | ------------ | ---------------- | ---------------- | ---- | ---------------------------------------------------------------------------------------------------------------------------- | | cif, cif2 | CIF | .cif | Atomic positions | Atomic positions | none | Experimental | | g, gromacs | Gromacs | .gro | Atomic positions | Atomic positions | none | Default format. | | m, mdview | MDView | .mdv | Atomic positions | Atomic positions | auto | | mdv_au | MDView | .mdv | Atomic positions | Atomic positions | auto | In atomic unit. | | o, openscad | OpenSCAD | .scad | Center of mass | none | o | See tests/art/openscad for usage. | | povray | Povray | .pov | Atomic positions | Atomic Positions | o | | towhee | TowHee | .coords(?) | Atomic positions | Atomic positions | none | | xyz | XYZ | .xyz | Atomic positions | Atomic positions | none | Experimental | | exyz | extended XYZ | .xyz | Atomic positions | Atomic positions | none | Extended XYZ format defined in Open Babel | | exyz2 | extended XYZ | .xyz | Atomic positions | Atomic positions | none | Extended XYZ format defined in QUIP | | y, yaplot | Yaplot | .yap | Atomic positions | Atomic positions | o | It renders molecular configurations and the HB network. | | 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, reshape | Python module | .py | Center of mass | none | none | Under development. | | _ringstat | Ring phase statistics | | | | | Statistical test suite 1: Check the appearance frequencies of the ring phases as a test for the intermediate-range disorder. | | rings | Yaplot | .yap | center of mass | none | o | It renders HB rings. | | _KG | Kirkwood G(r) | | | | | Statistical test suite 2: Calculate G(r) for checking long-range disorder in molecular orientations. |

By installing the genice2-mdanalysis package separately, you can generate files in many formats for a large number of molecular dynamics package softwares. E.g.

shell % pip install genice2-mdanalysis % genice2 1c -f 'mdanalysis[1c.pdb]' % genice2 1h -f 'mdanalysis[1h.xtc]'

All the supported file types are listed in the MDAnalysis web page.

You can prepare your file formats. Create a folder named formats in the current working directory and put the plugins in it.

Internally, there are seven stages to generate an ice structure.

1. Cell repetition.
2. Random graph generation and replication.
3. Apply ice rule.
4. Depolarize.
5. Determine orientations of the water molecules.
6. Place atoms in water molecules.
7. Place atoms in guests.

In the format plugin, you define the hook functions that are invoked after processing each stage.

Ice structures

| Symbol |

| | ------ | ------------------------------------------ |

0, ice0 | Metastable ice "0". [Russo 2014] 11, XI, ice11 | A candidate for an antiferroelectric Ice XI #19. [Jackson 1997, Fan 2010] 1152114, 12111, 14427301, 15124949650, 1532155471, 17625256, 20714435, 22623457, ACO, CS4, DDR, IWV, LTA, MAR, NON, PCOD8007225, PCOD8036144, PCOD8204698, PCOD8301974, PCOD8321499, PCOD8324623, SGT, SOD, engel01, engel03, engel04, engel17, engel20, engel23, engel24, engel26, engel29, engel30, engel31, engel34, sVII | Hypothetical zeolitic ice [Jeffrey 1984, Kosyakov 1999, Engel 2018, IZA Database] 11alt | A layered ferroelectric Ice XI. 11i | Sixteen candidates for Ice XI. [Hirsch 2004] 12, XII, ice12 | Metastable high-pressure ice XII. [Lobban 1998, Koza 2000] 13, XIII, ice13 | Ice XIII, a hydrogen-ordered counterpart of ice V. [Salzmann 2006] 14, ice14 | Ice XIV, a partially hydrogen-ordered counterpart of ice XII. Note that it does not reproduce the occupancies (probability of occupation) of the possible hydrogen sites. [Salzmann 2006] 16, CS2, MTN, XVI, ice16, sII | Ultralow-density Ice XVI. [Jeffrey 1984, Kosyakov 1999, Sikiric 2010, Falenty 2014, IZA Database] 17, XVII, ice17 | Ultralow-density Ice XVII. [Smirnov 2013, Rosso 2016, Strobel 2016] 1c, Ic, ice1c | Cubic type of ice I. [Vos 1993] 1h, Ih, ice1h | Most popular Ice I (hexagonal). NOTE: Due to a historical reason, the crystal axes of hexagonal ice are exchanged. If you want the basal plane to be Z axis, please use 'one[hh]' instead. 2, II, ice2 | Hydrogen-ordered ice II. [Kamb 1964, Londono 1988, Kamb 2003] 2D3 | Trilayer honeycomb ice. 2d, ice2d, ice2rect | A hydrogen-disordered counterpart of ice II. [Nakamura 2015] 3, III, ice3 | Ice III. [Petrenko 1999] 4, IV, ice4 | Ice IV. [Avogadro] 4R | Orthogonalized ice IV. [Avogadro] 5, V, ice5 | Monoclinic ice V (testing). 5R | Ice V with orthogonal unit cell. (testing) 6, VI, ice6 | Conventional high-pressure ice VI. [Petrenko 1999] 6h | Half lattice of ice VI. 7, VII, ice7 | Conventional high-pressure ice VII. 8, VIII, ice8 | Ice VIII, a hydrogen-ordered counterpart of ice VII. [Kuhs 1998] 9, IX, ice9 | Ice IX, a hydrogen-ordered counterpart of ice III. [Londono 1993] A, iceA | Hypothetical ice A. [Baez 1998] A15, Struct33 | Cubic Structure I of clathrate hydrate. [Sikiric 2010] B, iceB | Hypothetical ice B. [Baez 1998] BSV, engel05 | Hypothetical zeolitic ice of the gyroid structure. [Engel 2018, IZA Database] C14, C15, C36, FK6layers, FK9layers, HS2, Hcomp, Struct01, Struct03, Struct04, Struct05, Struct06, Struct07, Struct08, Struct09, Struct10, Struct11, Struct12, Struct13, Struct14, Struct15, Struct16, Struct17, Struct18, Struct19, Struct20, Struct21, Struct22, Struct23, Struct24, Struct25, Struct26, Struct27, Struct28, Struct29, Struct30, Struct31, Struct32, Struct34, Struct35, Struct36, Struct37, Struct38, Struct39, Struct40, Struct41, Struct42, Struct43, Struct44, Struct45, Struct46, Struct47, Struct48, Struct49, Struct50, Struct51, Struct52, Struct53, Struct54, Struct55, Struct56, Struct57, Struct58, Struct59, Struct60, Struct61, Struct62, Struct63, Struct64, Struct65, Struct66, Struct67, Struct68, Struct69, Struct70, Struct71, Struct72, Struct73, Struct74, Struct75, Struct76, Struct77, Struct78, Struct79, Struct80, Struct81, Struct82, Struct83, Struct84, Z, delta, mu, psigma, sV, sigma, zra-d | A space fullerene. [Sikiric 2010] CRN1, CRN2, CRN3 | A continuous random network of Sillium. [Mousseau 2001] CS1, MEP, sI | Clathrate hydrates sI. [Frank 1959, Jeffrey 1984, Kosyakov 1999, IZA Database] DOH, HS3, sH | Clathrate type H. EMT | Hypothetical ice with a large cavity. [Liu 2019, IZA Database] FAU | Hypothetical ice at negative pressure ice 'sIV'. [Huang 2017, IZA Database] HS1, sIV | Hydrogen-disordered ice Ih. [Kosyakov and Polyanskaya 1999] M, iceM | A hypothetical hydrogen-ordered high-density ice. [Mochizuki 2024] RHO | Hypothetical ice at negative pressure ice 'sIII'. [Huang 2016, IZA Database] Struct02 | A space fullerene. (I phase?) [Sikiric 2010] T | Hypothetical clathrate type T. [Sikiric 2010, Karttunen 2011] XIc-a | A candidate for the proton-ordered counterpart of ice Ic. The structure 'a' in Figure 1. [Geiger 2014] YKD | Ice in a d-surface (testing). [Kawano 2024] bilayer | A Bilayer Honeycomb Ice Phase in Hydrophobic Nanopores. [Koga 1997] c0te | Filled ice C0 by Teeratchanan (Hydrogen-disordered.) (Positions of guests are supplied.) [Teeratchanan 2015] c1te | Hydrogen-ordered hydrogen hydrate C1 by Teeratchanan. (Positions of guests are supplied.) [Teeratchanan 2015] c2te | Filled ice C2 (cubic ice) by Teeratchanan (Hydrogen disordered). (Positions of guests are supplied.) [Teeratchanan 2015] eleven | Ice XI w/ stacking faults. i | Hypothetical ice "i". [Fennell 2005] ice1hte | Filled ice Ih by Teeratchanan (Hydrogen disordered). (Positions of guests are supplied.) [Teeratchanan 2015] iceL | The hypothetical Ice L [Lei 2025] iceMd | A hydrogen-disordered counterpart of ice M. [Mochizuki 2024] iceR | Hypothetical ice R. [Maynard-Casely 2010, Mochizuki 2014] iceT | Hypothetical ice T. [Hirata 2017] iceT2 | Hypothetical ice T2. [Yagasaki 2018] one | Ice I w/ stacking disorder. oprism | Hydrogen-ordered ice nanotubes. [Koga 2001] sTprime | Filled ice sT'. [Smirnov 2013] xFAU | Aeroice xFAU. [Matsui 2017] xdtc | A porous ice with cylindrical channels. [Matsumoto 2021] 1hunit, TS1, dtc, ice1hunit, sIII | (Undocumented)

Ice names with double quotations are not experimentally verified.

You can prepare your own ice structures. Create a folder named lattices in the current working directory and put the plugins in it.

cif2ice is a tool to retrieve a cif file of zeolite from IZA structure database and prepare a lattice module in the path above.

Note: Different names are given in different nomenclature.

| CH/FI | CH | ice | FK | Zeo | Foam | | ----- | --- | --- | ----- | --- | ------------- | | sI | CS1 | - | A15 | MEP | Weaire-Phelan | | sII | CS2 | 16 | C15 | MTN | | | sIII | TS1 | - | sigma | - | | | sIV | HS1 | - | Z | - | | | sV | HS2 | - | * | - | | | sVII | CS4 | - | * | SOD | Kelvin | | sH | HS3 | - | * | DOH | | | C0 | - | 17 | * | - | | | C1 | - | 2 | * | - | | | C2 | - | 1c | * | - | |

FI: Filled ices; CH: Clathrate hydrates; FK:Frank-Kasper duals; Zeo: Zeolites; Foam: foam crystals (Weaire 1994).

-: No correspondence; *: Non-FK types.

Please ask vitroid@gmail.com to add new ice structures.

Water models

A water model can be chosen with --water option.

| symbol | type | | ------ | ---- |

3site, tip3p | A typical 3-site model. 4site, tip4p | A typical 4-site model. [Jorgensen 1983, Jorgensen 1985] 5site, tip5p | A typical 5-site model. 6site, NvdE | A 6-site water model. [Nada 2003] 7site | A seven-site water model. [Zhao 2019] physical_water | Physical model of water; Oxygen atom is on the lattice point. [Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983).] ice, spce | (Undocumented)

Guest molecules

| symbol | type | | ------ | ---- |

H2 | Hydrogen molecule. [https://www.britannica.com/science/hydrogen] ch4 | An all-atom methane model. et | A united-atom ethane model. me | A united-atom methane model. mol | Loader for MOL files (generated by MolView.org), e.g. mol[THF.mol]. thf | An all-atom tetrahydrofuran (THF) model. uathf | A united-atom five-site tetrahydrofuran (THF) model. co2, empty, g12, g14, g15, g16, one, uathf6 | (Undocumented)

You can prepare your own guest molecules. Create a folder named molecules in the current working directory and put the plugins in it.

Extra plugins

Some extra plugins are available via python package index using pip command.

For example, you can install RDF plugin by the following command,

shell % pip install genice2-rdf

And use it as an output format to get the radial distribution functions.

shell % genice2 TS1 -f _RDF > TS1.rdf.txt

Output and analysis plugins

Analysis plugin is a kind of output plugin (specified with -f option).

| pip name | GenIce2 option | Description | output format | requirements | | -------------------------------------------------------------------- | ---------------------- | ------------------------------------------------------------------------------------------------------------------- | ------------------------------------------- | ------------------------- | | genice2-cage | -f _cage | Detect cages and quasi-polyhedra (vitrites). | text, json, gromacs | cycless | | genice2-rdf | -f _RDF | Radial distribution functions. | text | | | genice2-svg | -f svg
-f png | 2D graphics in SVG format.
... in PNG format. | SVG
PNG | svgwrite | | genice2-twist | -f twist | Calculate the twist order parameter (and visualize) [Matsumoto 2019] | text (@BTWC)
SVG
PNG
yaplot | twist-op, genice2-svg | | genice2-mdanalysis | -f mdanalysis | Output the atoms in various file formats that are served by MDAnalysis. | text, binary | mdanalysis |

Input plugins

Input plugins (a.k.a. lattice plugins) construct a crystal structure on demand.

| pip name | GenIce2 usage | Description | requirements | | ------------------------------------------------------ | --------------------------------------------------- | --------------------------------------------------------------------------------- | ------------ | | genice2-cif | genice2 cif[ITT.cif]
genice2 zeolite[ITT] | Read a local CIF file as an ice structure.
Read a structure from Zeolite DB. | cif2ice |

New in GenIce2.1

GenIce2-MDAnalysis integration is now available. Try

shell % pip install genice2-mdanalysis % genice2 1h -r 4 4 4 -f "mdanalysis[1h.pdb]"

to generate a PDB file.

Changes from GenIce1

Novel algorithm to make a structure obeying the ice rules in Stage 3.

• We have devised a completely new algorithm for orienting water molecules so that they obey ice rules. This algorithm can be applied only to defect-free ice. The algorithm runs in the following steps.
  1. First, based on the distances between neighboring molecules, the structure of the hydrogen-bond network is represented by a 4-connected undirected graph.
  2. The undirected graph is then randomly tiled with cycles. That is, we draw many cycles in the network so that all edges belong to only one of the cycles. It is always possible to a 4-connected regular graph.
  3. By directing each cycle, we can immediately obtain a directed graph that satisfies the ice rule. We can choose two orientations for each cycle so that the total polarization of the entire system is as small as possible.
  4. In rare cases, complete depolarization may not be possible. In such cases, it is depolarized in Stage 4.

Faster, faster, faster.

Combinations of the new algorithm and other improvements in coding, the processing time of GenIce2 is about five times faster than that of GenIce1.

Core algorithm is separated.

The core part of the new algorithm is separated as the TileCycles package.

Colaboratory-ready!

Now GenIce2 works on the Google Colaboratory!

New ices

Many new ice structures are added.

Integration with MDAnalysis

GenIce2 is now integrated with MDAnalysis.

References

• [Avogadro] Avogadro https://github.com/cryos/avogadro/blob/master/crystals/ice/H2O-Ice-IV.cif

• [Baez 1998] BÁEZ, Luis A. and CLANCY, Paulette, 1995, Phase equilibria in extended simple point charge ice‐water systems. The Journal of Chemical Physics [online]. 8 December 1995. Vol. 103, no. 22, p. 9744–9755. DOI 10.1063/1.469938. Available from: http://dx.doi.org/10.1063/1.469938

• [Cockayne 1995] COCKAYNE, Eric, 1995. Dense quasiperiodic decagonal disc packing. Physical Review B [online]. 1 June 1995. Vol. 51, no. 21, p. 14958–14961. DOI 10.1103/physrevb.51.14958. Available from: http://dx.doi.org/10.1103/PhysRevB.51.14958

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• [Fan 2010] Xiaofeng Fan, Dan Bing, Jingyun Zhang, Zexiang Shen, Jer-Lai Kuo, Computational Materials Science 49 (2010) S170–S175.

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• [Geiger 2014] GEIGER, Philipp, DELLAGO, Christoph, MACHER, Markus, FRANCHINI, Cesare, KRESSE, Georg, BERNARD, Jürgen, STERN, Josef N. and LOERTING, Thomas, 2014. Proton Ordering of Cubic Ice Ic: Spectroscopy and Computer Simulations. The Journal of Physical Chemistry C. Online. 13 May 2014. Vol. 118, no. 20, p. 10989–10997. DOI 10.1021/jp500324x.

• [Hirata 2017] HIRATA, Masanori, YAGASAKI, Takuma, MATSUMOTO, Masakazu and TANAKA, Hideki, 2017, Phase Diagram of TIP4P/2005 Water at High Pressure. Langmuir [online]. 24 August 2017. Vol. 33, no. 42, p. 11561–11569. DOI 10.1021/acs.langmuir.7b01764. Available from: http://dx.doi.org/10.1021/acs.langmuir.7b01764

• [Hirsch 2004] Hirsch, T. K. & Ojamäe, L. Quantum-Chemical and Force-Field Investigations of Ice Ih: Computation of Proton-Ordered Structures and Prediction of Their Lattice Energies. J. Phys. Chem. B 108, 15856-15864 (2004)

• [Huang 2016] HUANG, Yingying, ZHU, Chongqin, WANG, Lu, CAO, Xiaoxiao, SU, Yan, JIANG, Xue, MENG, Sheng, ZHAO, Jijun and ZENG, Xiao Cheng, 2016, A new phase diagram of water under negative pressure: The rise of the lowest-density clathrate s-III. Science Advances [online]. February 2016. Vol. 2, no. 2, p. e1501010. DOI 10.1126/sciadv.1501010. Available from: http://dx.doi.org/10.1126/sciadv.1501010

• [Huang 2017] HUANG, Yingying, ZHU, Chongqin, WANG, Lu, ZHAO, Jijun and ZENG, Xiao Cheng, 2017, Prediction of a new ice clathrate with record low density: A potential candidate as ice XIX in guest-free form. Chemical Physics Letters [online]. March 2017. Vol. 671, p. 186–191. DOI 10.1016/j.cplett.2017.01.035. Available from: http://dx.doi.org/10.1016/j.cplett.2017.01.035

• [IZA Database] http://www.iza-structure.org/databases/

• [Jackson 1997] Jackson, S. M., V. M. Nield, R. W. Whitworth, M. Oguro, and C. C. Wilson, 1997, ‘‘Single-crystal neutron diffraction studies of the structure of ice XI,’’ J. Phys. Chem. B 101, 6142.

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• [Karttunen 2011] KARTTUNEN, Antti J., FÄSSLER, Thomas F., LINNOLAHTI, Mikko and PAKKANEN, Tapani A., 2011, Structural Principles of Semiconducting Group 14 Clathrate Frameworks. Inorganic Chemistry [online]. 7 March 2011. Vol. 50, no. 5, p. 1733–1742. DOI 10.1021/ic102178d. Available from: http://dx.doi.org/10.1021/ic102178d

• [Koga 1997] KOGA, Kenichiro, ZENG, X. C. and TANAKA, Hideki, 1997. Freezing of Confined Water: A Bilayer Ice Phase in Hydrophobic Nanopores. Physical Review Letters [online]. 29 December 1997. Vol. 79, no. 26, p. 5262–5265. DOI 10.1103/physrevlett.79.5262. Available from: http://dx.doi.org/10.1103/PhysRevLett.79.5262

• [Koga 2001] KOGA, Kenichiro, GAO, G. T., TANAKA, Hideki and ZENG, X. C., 2001, Formation of ordered ice nanotubes inside carbon nanotubes. Nature [online]. August 2001. Vol. 412, no. 6849, p. 802–805. DOI 10.1038/35090532. Available from: http://dx.doi.org/10.1038/35090532

• [Kosyakov 1999] KOSYAKOV, V. I. and POLYANSKAYA, T. M., 1999, Using structural data for estimating the stability of water networks in clathrate and semiclathrate hydrates. Journal of Structural Chemistry [online]. March 1999. Vol. 40, no. 2, p. 239–245. DOI 10.1007/bf02903652. Available from: http://dx.doi.org/10.1007/BF02903652

• [Koza 2000] KOZA, M. M., SCHOBER, H., HANSEN, T., TÖLLE, A. and FUJARA, F., 2000, Ice XII in Its Second Regime of Metastability. Physical Review Letters [online]. 1 May 2000. Vol. 84, no. 18, p. 4112–4115. DOI 10.1103/physrevlett.84.4112. Available from: http://dx.doi.org/10.1103/PhysRevLett.84.4112

• [Kuhs 1998] KUHS, W. F., FINNEY, J. L., VETTIER, C. and BLISS, D. V., 1984, Structure and hydrogen ordering in ices VI, VII, and VIII by neutron powder diffraction. The Journal of Chemical Physics [online]. 15 October 1984. Vol. 81, no. 8, p. 3612–3623. DOI 10.1063/1.448109. Available from: http://dx.doi.org/10.1063/1.448109

• [Liu 2019] LIU, Yuan, HUANG, Yingying, ZHU, Chongqin, LI, Hui, ZHAO, Jijun, WANG, Lu, OJAMÄE, Lars, FRANCISCO, Joseph S. and ZENG, Xiao Cheng, 2019, An ultralow-density porous ice with the largest internal cavity identified in the water phase diagram. Proceedings of the National Academy of Sciences [online]. 10 June 2019. Vol. 116, no. 26, p. 12684–12691. DOI 10.1073/pnas.1900739116. Available from: http://dx.doi.org/10.1073/pnas.1900739116

• [Lei 2025]

• [Lobban 1998] LOBBAN, C., FINNEY, J. L. and KUHS, W. F., 1998, The structure of a new phase of ice. Nature [online]. January 1998. Vol. 391, no. 6664, p. 268–270. DOI 10.1038/34622. Available from: http://dx.doi.org/10.1038/34622

• [Londono 1988] LONDONO, D., KUHS, W. F. and FINNEY, J. L., 1988, Enclathration of helium in ice II: the first helium hydrate. Nature [online]. March 1988. Vol. 332, no. 6160, p. 141–142. DOI 10.1038/332141a0. Available from: http://dx.doi.org/10.1038/332141a0

• [Londono 1993] LONDONO, J. D., KUHS, W. F. and FINNEY, J. L., 1993, Neutron diffraction studies of ices III and IX on under‐pressure and recovered samples. The Journal of Chemical Physics [online]. 15 March 1993. Vol. 98, no. 6, p. 4878–4888. DOI 10.1063/1.464942. Available from: http://dx.doi.org/10.1063/1.464942

• [Matsui 2017] MATSUI, Takahiro, HIRATA, Masanori, YAGASAKI, Takuma, MATSUMOTO, Masakazu and TANAKA, Hideki, 2017, Communication: Hypothetical ultralow-density ice polymorphs. The Journal of Chemical Physics [online]. 7 September 2017. Vol. 147, no. 9, p. 091101. DOI 10.1063/1.4994757. Available from: http://dx.doi.org/10.1063/1.4994757

• [Matsui 2019] MATSUI, Takahiro, YAGASAKI, Takuma, MATSUMOTO, Masakazu and TANAKA, Hideki, 2019, Phase diagram of ice polymorphs under negative pressure considering the limits of mechanical stability. The Journal of Chemical Physics [online]. 28 January 2019. Vol. 150, no. 4, p. 041102. DOI 10.1063/1.5083021. Available from: http://dx.doi.org/10.1063/1.5083021

• [Matsumoto 2019] MATSUMOTO, Masakazu, YAGASAKI, Takuma and TANAKA, Hideki, 2019, A Bayesian approach for identification of ice Ih, ice Ic, high density, and low density liquid water with a torsional order parameter. The Journal of Chemical Physics [online]. 7 June 2019. Vol. 150, no. 21, p. 214504. DOI 10.1063/1.5096556. Available from: http://dx.doi.org/10.1063/1.5096556

• [Matsumoto 2021] MATSUMOTO, Masakazu, YAGASAKI, Takuma and TANAKA, Hideki, 2021, Novel Algorithm to Generate Hydrogen-Disordered Ice Structures. Journal of Chemical Information and Modeling [online]. 24 May 2021. DOI 10.1021/acs.jcim.1c00440. Available from: http://dx.doi.org/10.1021/acs.jcim.1c00440

• [Maynard-Casely 2010] MAYNARD-CASELY, H. E., BULL, C. L., GUTHRIE, M., LOA, I., MCMAHON, M. I., GREGORYANZ, E., NELMES, R. J. and LOVEDAY, J. S., 2010, The distorted close-packed crystal structure of methane A. The Journal of Chemical Physics [online]. 14 August 2010. Vol. 133, no. 6, p. 064504. DOI 10.1063/1.3455889. Available from: http://dx.doi.org/10.1063/1.3455889

• [Mochizuki 2014] MOCHIZUKI, Kenji, HIMOTO, Kazuhiro and MATSUMOTO, Masakazu, 2014, Diversity of transition pathways in the course of crystallization into ice VII. Phys. Chem. Chem. Phys. [online]. 2014. Vol. 16, no. 31, p. 16419–16425. DOI 10.1039/c4cp01616e. Available from: http://dx.doi.org/10.1039/c4cp01616e

• [Mochizuki 2024] MOCHIZUKI, Kenji, 2024. Hydrogen Ordering in Ice Ih Facilitates the Transition from HDA to Ice XII. The Journal of Physical Chemistry C. Online. 16 October 2024. DOI 10.1021/acs.jpcc.4c05371.

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• [Nada 2003] Nada, Hiroki, and Jan P. J. M. van der Eerden. 2003. “An Intermolecular Potential Model for the Simulation of Ice and Water near the Melting Point: A Six-Site Model of H2O.” The Journal of Chemical Physics 118 (16): 7401–13.

• [Nakamura 2015] NAKAMURA, Tatsuya, MATSUMOTO, Masakazu, YAGASAKI, Takuma and TANAKA, Hideki, 2015, Thermodynamic Stability of Ice II and Its Hydrogen-Disordered Counterpart: Role of Zero-Point Energy. The Journal of Physical Chemistry B [online]. 3 December 2015. Vol. 120, no. 8, p. 1843–1848. DOI 10.1021/acs.jpcb.5b09544. Available from: http://dx.doi.org/10.1021/acs.jpcb.5b09544

• [Petrenko 1999] Petrenko and Whitworth, Physics of Ice, Table 11.2.

• [Rosso 2016] DEL ROSSO, Leonardo, CELLI, Milva and ULIVI, Lorenzo, 2016, New porous water ice metastable at atmospheric pressure obtained by emptying a hydrogen-filled ice. Nature Communications [online]. 7 November 2016. Vol. 7, no. 1. DOI 10.1038/ncomms13394. Available from: http://dx.doi.org/10.1038/ncomms13394

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• [Sikiric 2010] DUTOUR SIKIRIĆ, Mathieu, DELGADO-FRIEDRICHS, Olaf and DEZA, Michel, 2010, Space fullerenes: a computer search for new Frank–Kasper structures. Acta Crystallographica Section A Foundations of Crystallography [online]. 5 August 2010. Vol. 66, no. 5, p. 602–615. DOI 10.1107/s0108767310022932. Available from: http://dx.doi.org/10.1107/S0108767310022932

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Algorithms and how to cite them.

The algorithms to make a depolarized hydrogen-disordered ice are explained in these papers:

M. Matsumoto, T. Yagasaki, and H. Tanaka,"GenIce: Hydrogen-Disordered Ice Generator", J. Comput. Chem. 39, 61-64 (2017). DOI: 10.1002/jcc.25077

@article{Matsumoto:2017bk,
    author = {Matsumoto, Masakazu and Yagasaki, Takuma and Tanaka, Hideki},
    title = {GenIce: Hydrogen-Disordered Ice Generator},
    journal = {Journal of Computational Chemistry},
    volume = {39},
    pages = {61-64},
    year = {2017}
}

M. Matsumoto, T. Yagasaki, and H. Tanaka, “GenIce-core: Efficient algorithm for generation of hydrogen-disordered ice structures.”, J. Chem. Phys. 160, 094101 (2024). DOI:10.1063/5.0198056

@article{Matsumoto:2024,
    author = {Matsumoto, Masakazu and Yagasaki, Takuma and Tanaka, Hideki},
    title = {GenIce-core: Efficient algorithm for generation of hydrogen-disordered ice structures},
    journal = {Journal of Chemical Physics},
    volume = {160},
    pages = {094101},
    year = {2024}
}

How to contribute

GenIce has been available as open source software on GitHub(https://github.com/vitroid/GenIce) since 2015. Feedback, suggestions for improvements and enhancements, bug fixes, etc. are sincerely welcome. Developers and test users are also welcome. If you have any ice that is publicly available but not included in GenIce, please let us know.