GenIce 1.0rc5

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

GenIce

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

version 1.0rc5

Requirements

• networkx>=2
• countrings>=0.1.5
• pairlist>=0.2.3
• yaplotlib>=0.1
• numpy

Installation

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

pip3 install genice

Uninstallation

pip3 uninstall genice

Usage

usage: genice [-h] [--version] [--rep REP REP REP] [--dens DENS]
              [--add_noise percent] [--seed SEED] [--format gmeqdypoc]
              [--water model] [--guest D=empty] [--Guest 13=me]
              [--Group 13=bu-:0] [--anion 3=Cl] [--cation 3=Na]
              [--visual visual] [--nodep] [--asis] [--debug] [--quiet]
              Type

GenIce is a swiss army knife to generate hydrogen-disordered ice structures.
(version 1.0rc5)

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
  --version, -V         show program's version number and exit
  --rep REP REP REP, -r REP REP REP
                        Repeat the unit cell in x,y, and z directions. [1,1,1]
  --dens DENS, -d DENS  Specify the ice density in g/cm3
  --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 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)]
                        [gromacs]
  --water model, -w model
                        Specify water model. (tip3p, tip4p, etc.) [tip3p]
  --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.)
  --visual visual       Specify the yaplot file to store the depolarization
                        paths. [""]
  --nodep               No depolarization.
  --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.

Use ./genice.x instead of genice if you want to use GenIce without installation.

Examples

• 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
  

Basics

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 -s option 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 x option to specify the density in g cm^-3.

    genice 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 own 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)

    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.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:

    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. 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.

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.

Semiclathrate hydrates

Placement of a tetrabutylammonium ion

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.

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.

AnalIce command

AnalIce is a variant of GenIce. AnalIce reads a Gromacs file and do not modify the molecular orientation or the hydrogen bond network topology. AnalIce is prepared to use it for structure analysis.

For example, if you want to see the ring statistic of a given .gro file, use like this:

analice input.gro -f _ringstat

If you want to replace water model from the original three-site one (described as OW, HW1, and HW2) to TIP4P-like four-site model, try

analice input.gro -O OW -H HW[12] -w tip4p 

All the output formats are also available for AnalIce.

More examples

Load every 10 frames from a set of .gro files and output ring statistics in separate files.

analice '%05d.gro' --framerange 0:1000000:10 -O OW -H HW[12] --format _ringstat -o '%04d.rstat'

Make V-structures (removal of quick librational motion of water) from the given set of .gro files.

analice '%05d.gro' -O OW -H HW[12] -w tip3p --avgspan 25 > vstruct.gro

Usage of analice

usage: analice [options]

GenIce is a swiss army knife to generate hydrogen-disordered ice structures.
(version 1.0rc5)

positional arguments:
  File                  Input file(s). Analice accepts `.gro` (Gromacs),
                        `.mdv` (mdview), and `.nx3a` (rigid rotors) files as
                        input file formats by default. File type is estimated
                        from the suffix. Files of different types cannot be
                        read at a time. File type can be specified explicitly
                        with -s option.

optional arguments:
  -h, --help            show this help message and exit
  --version, -V         show program's version number and exit
  --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)]
                        [gromacs]
  --output %04d.gro, -o %04d.gro
                        Output in separate files.
  --water model, -w model
                        Replace water model. (tip3p, tip4p, etc.) [tip3p]
  --oxygen OW, -O OW    Specify atom name of oxygen in input Gromacs file.
                        ("O")
  --hydrogen HW[12], -H HW[12]
                        Specify atom name (regexp) of hydrogen in input
                        Gromacs file. ("H")
  --suffix gro, -s gro  Specify the file suffix explicitly. ((None)
  --filerange [from:]below[:interval]
                        Specify the number range for the input filename.
                        ("0:1000000")
  --framerange [from:]below[:interval]
                        Specify the number range for the input frames.
                        ("0:1000000")
  --debug, -D           Output debugging info.
  --quiet, -q           Do not output progress messages.
  --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.
  --avgspan 1, -v 1     Output mean atomic positions of a given time span so
                        as to remove fast librational motions and to make a
                        smooth video. The values 0 and 1 specify no averaging.

Output formats (genice and analice)

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.

You can prepare your own file formats. Create a folder named formats in the current working directory and put the plugins in it. GenIce 1.0 no longer refers the files in ~/.genice folder.

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 (genice only)

Symbol	Description
1h, ice1h, Ih	Most popular Ice I (hexagonal)
1c, ice1c, Ic	Cubic type of ice I
2, ice2, II	Hydrogen-ordered ice II
2d, ice2d	Hypothetical Hydrogen-disordered Ice II.[Nakamura 2015]
3, ice3, III	Conventional high-pressure ice III.[Lobban 1998]
4, ice4, IV	Metastable high-pressure ice IV.[Lobban 1998]
4R	Ice IV with orthogonal unit cell. (testing)
5, ice5, V	Monoclinic ice V (testing).
5R	Ice V with orthogonal unit cell. (testing)
6, ice6, VI	Conventional high-pressure ice VI.[Lobban 1998]
6h	Half lattice of ice IV.
7, ice7, VII	Conventional high-pressure ice VII.[Lobban 1998]
8, ice8, VIII	Ice VIII, a hydrogen-ordered counterpart of ice VII.[Kuhs 1998]
9, ice9, IX	Ice IX, a hydrogen-ordered counterpart of ice III.[Londono 1993]
12, ice12, XII	Metastable high-pressure ice XII.[Lobban 1998]
13, ice13, XIII	Ice XIII, a hydrogen-ordered counterpart of ice V.[Salzmann 2006]
16, ice16, XVI	Negative-pressure ice XVI.[Falenty 2014]
17, ice17, XVII	Negative-pressure ice XVII.[del Rosso 2016]
0, ice0	Hypothetical ice "0".[Russo 2014]
i	Hypothetical ice "i". = Zeolite BCT.[Fennell 2005]
A, iceA	Hypothetical hydrogen-ordered ices "A" and "B".[Baez 1998]
B, iceB	Hypothetical hydrogen-ordered ices "A" and "B".[Baez 1998]
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]
EMT	Hypothetical ice with a large cavity.[Liu 2019]
DOH,MEP,MTN,SOD	Aliases of HS3, CS1, CS2, and CS4, respectively.
CRN1,CRN2,CRN3	4-coordinated continuous random network [Mousseau 2005]
Struct01 .. Struct84	Space Fullerenes [Dutour Sikiric 2010]
A15, sigma, Hcomp, Kcomp, Z, mu, zra-d, FK9layers, FK6layers, 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]
xFAU[2], xFAU[4], xFAU[16], ...	Aeroices, i.e. extended FAU.[Matsui 2017]
xFAU2[2], xFAU2[4], xFAU2[16], ...	Aeroices, i.e. extended FAU.[Matsui 2017] (Hydrogen bond orientations are modified.)
iceR	Partial plastic ice R [Mochizuki 2014].
iceT	Partial plastic ice T [Hirata 2017].
iceT2	Partial plastic ice T2 [Yagasaki 2018].
dtc	Ultralow-density ice containing cylindrical pores. [Matsui 2019]
prism[4], prism[5], prism[6], ...	Ice nanotubes. [Koga 2001].

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. GenIce 1.0 no longer refers the files in ~/.genice folder.

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: 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.

Please ask [e-mail] to add new ice structures.

Water models (genice and analice)

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

Guest molecules (genice only)

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.

You can prepare your own guest molecules. Create a folder named molecules in the current working directory and put the plugins in it. GenIce 1.0 no longer refers the files in ~/.genice folder.

Input files (analice only)

suffix	type
gro	Gromacs
mdv	mdview (Angstrom)
mdva	mdview (au)
nx3a	Rigid rotors (with euler angles)

You can prepare your own file loaders. Create a folder named loaders in the current working directory and put the plugins in it. The plugin name is refered as the suffix of the file. (e.g. prepare pdb.py to load a *.pdb file.)

Extra plugins

(New in v1.0)

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

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

% pip install genice-rdf

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

% genice TS1 -f _RDF > TS1.rdf.txt

Output and analysis plugins

Analysis plugin is a kind of output plugin (specified with -f option). They are useful with analice command.

pip name	GenIce option	Description	output format	requirements
genice-rdf	-f _RDF	Radial distribution functions.	text
genice-svg	-f svg -f png	2D graphics in SVG format. ... in PNG format.	SVG PNG	svgwrite
genice-vpython	-f vpython	Display the structure in the browser using VPython.	(none)	vpython
genice-twist	-f twist	Calculate the twist order parameter (and visualize) [Matsumoto 2019]	text (@BTWC) SVG PNG yaplot	twist-op, genice-svg

Input plugins

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

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

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Algorithm and how to cite it.

The algorithm to make a depolarized hydrogen-disordered ice is explained in our recent paper:

M. Masakazu, 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}
}

How to contribute

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. Please let us know if there are ices that have been published but is not in GenIce.