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A swiss army knife to generate proton-disordered ice structures.

License: MIT License

Python 87.23% Makefile 0.22% Shell 0.01% Jupyter Notebook 12.53% Gnuplot 0.01%

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xuw10 andrewhuynguyen python3pkg andreanelli antiphoton gbarbalinardo aximthered jingxiangguo asymmetrical-1024 apachehigh5 nileshjchoudhary yychuang yongdatasci kavini1995 fujiepku georanius chw90 rusl2019 jjiang-amoy

genice's Issues

Missing guest molecules in sH structure

Hi,

it seems the sH clathrate structure doesn't include the cages information in genice/lattices/sH.py so it won't have guest molecules in the generated structure.
(This was my command line:
genice --rep 2 2 2 --seed 0 --format=exyz --water tip3p -g 12=ch4 sH)

I was wondering if the information for the cages could be added.

Many thanks,
Eszter

Ice 3 depolarization stuck

Hello there, a very nice and helpful programme you have made, thank you!

I'm not sure whether there is a fundamental reason behind it, but when I'm trying to produce a single ice 3 structure using "genice ice3 > test.gro" it gets stuck at "INFO Net polarization: [0.00 -0.00 2.00]". It's working fine when I include '--rep 2 2 2' or '--rep 3 3 3'. If there is a fundamental reason behind it, I guess it would be useful with a warning like on ice 7 and 8, when trying to produce a single cell. I've attached the output at the bottom FYI.

Thanks a lot!
//Tor

genice ice3 > test.gro
INFO Load lattice module 'ice3', arguments []
INFO
INFO Command line: /anaconda3/bin/genice ice3
INFO No rotmatrices in lattice
INFO Cell dimension:
INFO a = 6.666
INFO b = 6.666
INFO c = 6.936
INFO A = 90.0
INFO B = 90.0
INFO C = 90.0
INFO HB connectivity is not defined.
INFO Bond length (specified): 3.0
INFO Target Density: 1.165
INFO Original Density: 0.0011637864512692793
INFO Bond length (scaled, nm): 0.2998957965366282
INFO Load format module 'gromacs', arguments []
INFO Stage1: Replication.
INFO Number of water molecules: 12
INFO Pairs are not given explicitly.
INFO Estimating the bonds according to the pair distances.
INFO Number of water nodes: 12
INFO Cell dimension:
INFO a = 0.6663684599043879
INFO b = 0.6663684599043879
INFO c = 0.6933590815926843
INFO A = 90.0
INFO B = 90.0
INFO C = 90.0
INFO Stage1: end.
INFO Stage2: Graph preparation.
INFO Number of pre-oriented hydrogen bonds: 0
INFO Number of unoriented hydrogen bonds: 24
INFO Number of hydrogen bonds: 24 (regular num: 24)
INFO Stage2: end.
INFO Stage3: Bernal-Fowler rule.
INFO Defects remaining: 11
INFO Defects remaining: 8
INFO Defects remaining: 4
INFO Defects remaining: 2
INFO Defects remaining: 1
INFO Defects remaining: 0
INFO Stage3: end.
INFO Stage4: Depolarization.
INFO Non Z4: []
INFO Net polarization: [-2.00 2.00 2.00]
INFO Net polarization: [0.00 2.00 2.00]
INFO Net polarization: [0.00 -0.00 2.00]
^CTraceback (most recent call last):
File "/anaconda3/bin/genice", line 8, in
sys.exit(main())
File "/anaconda3/lib/python3.6/site-packages/genice/main.py", line 114, in main
depolarize=depolarize,
File "/anaconda3/lib/python3.6/site-packages/genice/genice.py", line 765, in generate_ice
record_depolarization_path=record_depolarization_path)
File "/anaconda3/lib/python3.6/site-packages/genice/genice.py", line 959, in stage4
dg.depolarize(self.spacegraph, self.repcell.mat, draw=None)
File "/anaconda3/lib/python3.6/site-packages/genice/digraph.py", line 501, in depolarize
cycle = traversing_cycle(spaceicegraph, cell, axis, draw)
File "/anaconda3/lib/python3.6/site-packages/genice/digraph.py", line 405, in traversing_cycle
logger.debug("Dipole of the path2: {0}".format(spaceicegraph.dipole_moment(path2)))
File "/anaconda3/lib/python3.6/site-packages/genice/digraph.py", line 319, in dipole_moment
for i in range(len(order) - 1):
KeyboardInterrupt
INFO Completed.

Coordinates Swapped When Generating Ih Gro file

When generating a .gro file of an Ih ice slab with a tip4p water model using genice the coordinates system were switched around such that what was x should be y what was y should be z and what was z should be x.

Using this exact code in Colab:
from genice2.genice import GenIce
from genice2.plugin import Lattice, Format, Molecule

lattice = Lattice("Ih")
formatter = Format("gromacs")
water = Molecule("tip4p")
ice = GenIce(lattice, rep=[8,8,6]).generate_ice(water, formatter)
print(ice)

Visualizing this file in VMD the basal facet (which should be in the z direction) was in the y direction

[Bug] GenIce2 cannot generate some ices

Hello dr. Masakazu Matsumoto, I would like to report a bug when generating some ices.

Here's a list of the ices:

ice2
ice7
ice8
ice11
ice13

When I generate ice2, I get the output:

ruslan@neptunus:~/Documents/genice-test$ genice2 ice2 --rep 3 3 3 --seed 1234 --format gromacs --water ice --depol=optimal > conf.gro

INFO main: end.
INFO main: 403 ms
Traceback (most recent call last):
  File "/home/ruslan/.local/bin/genice2", line 8, in <module>
    sys.exit(main())
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 14, in _time_it
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 34, in _banner
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/cli/genice.py", line 201, in main
    lat = GenIce(safe_import("lattice", lattice_type).Lattice(**lattice_options),
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/lattices/ice2.py", line 60, in __init__
    self.waters, self.fixed = CIF.waters_and_pairs(self.cell, atomd, sops)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/CIF.py", line 125, in waters_and_pairs
    for i, j in pl.pairs_iter(oxygens,
TypeError: pairs_iter() got an unexpected keyword argument 'rc'

ruslan@neptunus:~/Documents/genice-test$

I also tried some tests using the cif and zeolite plugins, getting the following output:

plugin zeolite

ruslan@neptunus:~/Documents/genice-test$ genice2 zeolite[EDI] --rep 3 3 3 --seed 1234 --format gromacs --water ice --depol=optimal > conf.gro

INFO Extra lattice plugin: zeolite
INFO EDI
INFO Input: EDI.cif
WARNING could not convert "T1" into element name!
WARNING could not convert "T2" into element name!
INFO Loaded a CIF file with 5 atom coordinates and 8 symmetry operations.
INFO Created a unit cell consisting of 15 atoms.
INFO Fractional coordinates:
INFO         T2  0.000  0.000  0.500
INFO         T1  0.000  0.732  0.882
INFO         T1  0.732  0.000  0.118
INFO         T1  0.000  0.268  0.882
INFO         T1  0.268  0.000  0.118
INFO          O  0.000  0.500  0.882
INFO          O  0.190  0.810  0.000
INFO          O  0.810  0.810  0.000
INFO          O  0.810  0.190  0.000
INFO          O  0.000  0.810  0.645
INFO          O  0.810  0.000  0.355
INFO          O  0.000  0.190  0.645
INFO          O  0.500  0.000  0.118
INFO          O  0.190  0.190  0.000
INFO          O  0.190  0.000  0.355
INFO Cell volume: 307.48434116 (calc.), 0 (data)
INFO __init__: Constructor of GenIce.
INFO   
INFO   Command line: /home/ruslan/.local/bin/genice2 zeolite[EDI] --rep 3 3 3 --seed 1234 --format gromacs --water ice --depol=optimal
INFO No rotmatrices in lattice
INFO Cell dimension:
INFO   a = 6.926
INFO   b = 6.926
INFO   c = 6.41
INFO   A = 90.0
INFO   B = 90.0
INFO   C = 90.0
INFO HB connectivity is not defined.
INFO __init__: end.
INFO __init__: 3 ms
INFO main: end.
INFO main: 1355 ms
Traceback (most recent call last):
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/genice.py", line 534, in __init__
    self.bondlen = lat.bondlen
AttributeError: 'Lattice' object has no attribute 'bondlen'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ruslan/.local/bin/genice2", line 8, in <module>
    sys.exit(main())
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 14, in _time_it
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 34, in _banner
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/cli/genice.py", line 201, in main
    lat = GenIce(safe_import("lattice", lattice_type).Lattice(**lattice_options),
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 14, in _time_it
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 34, in _banner
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/genice.py", line 540, in __init__
    p = pl.pairs_iter(self.waters,
TypeError: pairs_iter() got an unexpected keyword argument 'rc'
INFO Completed.

ruslan@neptunus:~/Documents/genice-test$

plugin cif

ruslan@neptunus:~/Documents/genice-test$ genice2 cif[EDI.cif] --rep 3 3 3 --seed 1234 --format gromacs --water ice --depol=optimal > conf.gro

INFO Extra lattice plugin: cif
INFO EDI.cif
INFO Input: EDI.cif
WARNING could not convert "T1" into element name!
WARNING could not convert "T2" into element name!
INFO Loaded a CIF file with 5 atom coordinates and 8 symmetry operations.
INFO Created a unit cell consisting of 15 atoms.
INFO Fractional coordinates:
INFO         T2  0.000  0.000  0.500
INFO         T1  0.000  0.732  0.882
INFO         T1  0.732  0.000  0.118
INFO         T1  0.000  0.268  0.882
INFO         T1  0.268  0.000  0.118
INFO          O  0.000  0.500  0.882
INFO          O  0.190  0.810  0.000
INFO          O  0.810  0.810  0.000
INFO          O  0.810  0.190  0.000
INFO          O  0.000  0.810  0.645
INFO          O  0.810  0.000  0.355
INFO          O  0.000  0.190  0.645
INFO          O  0.500  0.000  0.118
INFO          O  0.190  0.190  0.000
INFO          O  0.190  0.000  0.355
INFO Cell volume: 307.48434116 (calc.), 0 (data)
INFO __init__: Constructor of GenIce.
INFO   
INFO   Command line: /home/ruslan/.local/bin/genice2 cif[EDI.cif] --rep 3 3 3 --seed 1234 --format gromacs --water ice --depol=optimal
INFO No rotmatrices in lattice
INFO Cell dimension:
INFO   a = 6.926
INFO   b = 6.926
INFO   c = 6.41
INFO   A = 90.0
INFO   B = 90.0
INFO   C = 90.0
INFO HB connectivity is not defined.
INFO __init__: end.
INFO __init__: 2 ms
INFO main: end.
INFO main: 332 ms
Traceback (most recent call last):
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/genice.py", line 534, in __init__
    self.bondlen = lat.bondlen
AttributeError: 'Lattice' object has no attribute 'bondlen'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/ruslan/.local/bin/genice2", line 8, in <module>
    sys.exit(main())
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 14, in _time_it
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 34, in _banner
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/cli/genice.py", line 201, in main
    lat = GenIce(safe_import("lattice", lattice_type).Lattice(**lattice_options),
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 14, in _time_it
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/decorators.py", line 34, in _banner
    return func(*args, **kwargs)
  File "/home/ruslan/.local/lib/python3.8/site-packages/genice2/genice.py", line 540, in __init__
    p = pl.pairs_iter(self.waters,
TypeError: pairs_iter() got an unexpected keyword argument 'rc'
INFO Completed.

ruslan@neptunus:~/Documents/genice-test$

GenIce version and Platform

OS = CentOS 7 & Rocky Linux 8
Python-installer = Anaconda3-2020.11
Python-version = Python 3.8.5
Pip-version = pip 20.2.4
GenIce-version = genice2 2.1.5

Can genice2 generate top file of gromacs? many thanks!

cannot generate some ices. Problem with one & prism

Love genice!

And it seems to be working beautifully for most of the ices, but I seem to be running to a problem with some ices.

I am on a macOS 11.4 - not sure if makes a difference?

(base) ~/D/s/f/ices ❯❯❯ genice2 prism
INFO Prism ice with 6 sides and 10 rows.
INFO __init__: Constructor of GenIce.
INFO   
INFO   Generate a prism ice.
INFO   
INFO   Options:
INFO     rows=r
INFO     sides=s
INFO       
INFO   
INFO   Command line: /Users/valentina/opt/anaconda3/bin/genice2 prism
INFO No rotmatrices in lattice
INFO Cell dimension:
INFO   a = 55.0
INFO   b = 55.0
INFO   c = 27.5
INFO   A = 90.0
INFO   B = 90.0
INFO   C = 90.0
INFO HB connectivity is not defined.
INFO Bond length (specified): 3
INFO Target Density: 0.0215588172693113
INFO Original Density: 2.1558817269311263e-05
INFO Bond length (scaled, nm): 0.2999999999999998
INFO __init__: end.
INFO __init__: 2 ms
INFO Stage1: Replicate water molecules to make a repeated cell.
INFO   Number of water molecules: 60
INFO   Pairs are not given explicitly.
INFO   Estimating the bonds according to the pair distances.
INFO   Number of water nodes: 60
INFO Cell dimension:
INFO   a = 5.499999999999997
INFO   b = 5.499999999999997
INFO   c = 2.7499999999999987
INFO   A = 90.0
INFO   B = 90.0
INFO   C = 90.0
INFO Stage1: end.
INFO Stage1: 3 ms
INFO Stage2: Make a random graph and replicate.
INFO Stage2: end.
INFO Stage2: 2 ms
INFO   Number of pre-oriented hydrogen bonds: 0
INFO   Number of unoriented hydrogen bonds: 120
INFO   Number of hydrogen bonds: 120 (regular num: 120)
INFO Stage3D: Tile the graph with directed cycles.
INFO spanningCycles: Look up the traversal cycles.
INFO spanningCycles: end.
INFO spanningCycles: 1 ms
INFO direct: Re-orient the cycles so as to minimize the net polarization.
INFO direct: end.
INFO direct: 0 ms
INFO Stage3D: end.
INFO Stage3D: 2 ms
INFO main: end.
INFO main: 23 ms
Traceback (most recent call last):
  File "/Users/valentina/opt/anaconda3/bin/genice2", line 8, in <module>
    sys.exit(main())
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/decorators.py", line 14, in _time_it
    return func(*args, **kwargs)
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/decorators.py", line 34, in _banner
    return func(*args, **kwargs)
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/cli/genice.py", line 252, in main
    result = lat.generate_ice(water=water,
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/genice.py", line 759, in generate_ice
    abort = Stages()
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/genice.py", line 720, in Stages
    self.Stage3D()
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/decorators.py", line 14, in _time_it
    return func(*args, **kwargs)
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/decorators.py", line 34, in _banner
    return func(*args, **kwargs)
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/genice.py", line 1057, in Stage3D
    dir = direct(dipoles, spanning)
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/decorators.py", line 14, in _time_it
    return func(*args, **kwargs)
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/decorators.py", line 34, in _banner
    return func(*args, **kwargs)
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/genice.py", line 1016, in direct
    pol2 = pol @ pol
TypeError: unsupported operand type(s) for @: 'numpy.float64' and 'numpy.float64'
INFO Completed.

(base) ~/D/s/f/ices ❯❯❯ genice2 one                                                           ✘ 1 
INFO main: end.
INFO main: 4 ms
Traceback (most recent call last):
  File "/Users/valentina/opt/anaconda3/bin/genice2", line 8, in <module>
    sys.exit(main())
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/decorators.py", line 14, in _time_it
    return func(*args, **kwargs)
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/decorators.py", line 34, in _banner
    return func(*args, **kwargs)
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/cli/genice.py", line 214, in main
    safe_import(
  File "/Users/valentina/opt/anaconda3/lib/python3.8/site-packages/genice2/lattices/one.py", line 31, in __init__
    for ch in arg:
UnboundLocalError: local variable 'arg' referenced before assignment

bug:when generating 6site-ice ,the structual of water molecule is wrong

bug:when generating 6site-ice ,the structual of water molecule is wrong
usage: genice --water 6site --format g Ih > 6siteIh16.gro

I found the distance between O and other atom in the same 6site-water molecule is ten times that of correct one.

Problem about install Genice package_pairlist package can not be installed

Dear Professor Masakazu Matsumoto

First Thank you so much to develop such a package to generate ice structure. It is very helpful for people who wants to do some work about simulations on clathrate hydrates and ice lattices, especially for me, a complete beginner.

But actually I have some trouble at the very beginning, that is to install the GenIce package on my computer (Window 10). I use Python 3.5, "pip3 install GenIce", and everything is Ok, but the package " Pairlist "that GenIce needed can not be installed successfully. I try my best to Google the issue and find the possible answer, but failed. I dont know where I was wrong. Is it the problem of the environment of my computer, or something else？

Thank you for taking your time and hope your valuable advice.

ps: i guess that using the pairlist. whl to install is a solver, but i see on https://pypi.org/ there is only .whl for macosx. no a window type.

Here is the Error information when i installed GenIce：

(python35) C:\Users\Administrator>pip install GenIce
Collecting GenIce
Using cached GenIce-1.0.10-py2.py3-none-any.whl (696 kB)
Requirement already satisfied: countrings>=0.1.7 in d:\ana\envs\python35\lib\site-packages (from GenIce) (0.1.7)
Requirement already satisfied: numpy in d:\ana\envs\python35\lib\site-packages (from GenIce) (1.13.1)
Collecting pairlist>=0.2.3
Using cached PairList-0.2.9.tar.gz (8.9 kB)
Requirement already satisfied: networkx>=2 in d:\ana\envs\python35\lib\site-packages (from GenIce) (2.4)
Requirement already satisfied: yaplotlib>=0.1 in d:\ana\envs\python35\lib\site-packages (from GenIce) (0.1.2)
Requirement already satisfied: methodtools in d:\ana\envs\python35\lib\site-packages (from countrings>=0.1.7->GenIce) (0.1.3)
Requirement already satisfied: decorator>=4.3.0 in d:\ana\envs\python35\lib\site-packages (from networkx>=2->GenIce) (4.4.2)
Requirement already satisfied: wirerope==0.3.1 in d:\ana\envs\python35\lib\site-packages (from methodtools->countrings>=0.1.7->GenIce) (0.3.1)
Requirement already satisfied: six>=1.11.0 in d:\ana\envs\python35\lib\site-packages (from wirerope==0.3.1->methodtools->countrings>=0.1.7->GenIce) (1.15.0)
Building wheels for collected packages: pairlist
Building wheel for pairlist (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: 'd:\ana\envs\python35\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\ADMINI1\AppData\Local\Temp\pip-install-k93z0ykf\pairlist\setup.py'"'"'; file='"'"'C:\Users\ADMINI1\AppData\Local\Temp\pip-install-k93z0ykf\pairlist\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d 'C:\Users\ADMINI1\AppData\Local\Temp\pip-wheel-cfc2e980'
cwd: C:\Users\ADMINI1\AppData\Local\Temp\pip-install-k93z0ykf\pairlist
Complete output (56 lines):
running bdist_wheel
running build
running build_py
creating build
creating build\lib.win-amd64-3.5
copying pairlist.py -> build\lib.win-amd64-3.5
running build_ext
No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
building 'cpairlist' extension
creating build\temp.win-amd64-3.5
creating build\temp.win-amd64-3.5\Release
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Id:\ana\envs\python35\lib\site-packages\numpy\core\include -Id:\ana\envs\python35\include -Id:\ana\envs\python35\include -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" /Tccpairlist.c /Fobuild\temp.win-amd64-3.5\Release\cpairlist.obj -std=c99
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Id:\ana\envs\python35\lib\site-packages\numpy\core\include -Id:\ana\envs\python35\include -Id:\ana\envs\python35\include -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" /Tcpairlist.c /Fobuild\temp.win-amd64-3.5\Release\pairlist.obj -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
pairlist.c
pairlist.c: warning C4819: The file contains a character that cannot be represented in the current code page (936). Save the file in Unicode format to prevent data loss
pairlist.c(106): error C2057: expected constant expression
pairlist.c(106): error C2466: cannot allocate an array of constant size 0
pairlist.c(106): error C2133: 'nResidents': unknown size
pairlist.c(114): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(122): error C2057: expected constant expression
pairlist.c(122): error C2466: cannot allocate an array of constant size 0
pairlist.c(122): error C2133: 'residents': unknown size
pairlist.c(123): error C2057: expected constant expression
pairlist.c(123): error C2466: cannot allocate an array of constant size 0
pairlist.c(123): error C2133: 'heads': unknown size
pairlist.c(124): error C2057: expected constant expression
pairlist.c(124): error C2466: cannot allocate an array of constant size 0
pairlist.c(124): error C2133: 'pointer': unknown size
pairlist.c(137): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(245): error C2057: expected constant expression
pairlist.c(245): error C2466: cannot allocate an array of constant size 0
pairlist.c(245): error C2133: 'nResidents0': unknown size
pairlist.c(246): error C2057: expected constant expression
pairlist.c(246): error C2466: cannot allocate an array of constant size 0
pairlist.c(246): error C2133: 'nResidents1': unknown size
pairlist.c(256): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(268): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(279): error C2057: expected constant expression
pairlist.c(279): error C2466: cannot allocate an array of constant size 0
pairlist.c(279): error C2133: 'pointer': unknown size
pairlist.c(282): error C2057: expected constant expression
pairlist.c(282): error C2466: cannot allocate an array of constant size 0
pairlist.c(282): error C2133: 'residents0': unknown size
pairlist.c(283): error C2057: expected constant expression
pairlist.c(283): error C2466: cannot allocate an array of constant size 0
pairlist.c(283): error C2133: 'heads0': unknown size
pairlist.c(297): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(303): error C2057: expected constant expression
pairlist.c(303): error C2466: cannot allocate an array of constant size 0
pairlist.c(303): error C2133: 'residents1': unknown size
pairlist.c(304): error C2057: expected constant expression
pairlist.c(304): error C2466: cannot allocate an array of constant size 0
pairlist.c(304): error C2133: 'heads1': unknown size
pairlist.c(321): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
error: Command "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Id:\ana\envs\python35\lib\site-packages\numpy\core\include -Id:\ana\envs\python35\include -Id:\ana\envs\python35\include -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" /Tcpairlist.c /Fobuild\temp.win-amd64-3.5\Release\pairlist.obj -std=c99" failed with exit status 2

ERROR: Failed building wheel for pairlist
Running setup.py clean for pairlist
Failed to build pairlist
Installing collected packages: pairlist, GenIce
Running setup.py install for pairlist ... error
ERROR: Command errored out with exit status 1:
command: 'd:\ana\envs\python35\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\ADMINI~~1\AppData\Local\Temp\pip-install-k93z0ykf\pairlist\setup.py'"'"'; file='"'"'C:\Users\ADMINI~~1\AppData\Local\Temp\pip-install-k93z0ykf\pairlist\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\ADMINI1\AppData\Local\Temp\pip-record-2s0kfk7e\install-record.txt' --single-version-externally-managed --compile --install-headers 'd:\ana\envs\python35\Include\pairlist'
cwd: C:\Users\ADMINI1\AppData\Local\Temp\pip-install-k93z0ykf\pairlist
Complete output (56 lines):
running install
running build
running build_py
creating build
creating build\lib.win-amd64-3.5
copying pairlist.py -> build\lib.win-amd64-3.5
running build_ext
No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
building 'cpairlist' extension
creating build\temp.win-amd64-3.5
creating build\temp.win-amd64-3.5\Release
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Id:\ana\envs\python35\lib\site-packages\numpy\core\include -Id:\ana\envs\python35\include -Id:\ana\envs\python35\include -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" /Tccpairlist.c /Fobuild\temp.win-amd64-3.5\Release\cpairlist.obj -std=c99
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Id:\ana\envs\python35\lib\site-packages\numpy\core\include -Id:\ana\envs\python35\include -Id:\ana\envs\python35\include -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" /Tcpairlist.c /Fobuild\temp.win-amd64-3.5\Release\pairlist.obj -std=c99
cl : Command line warning D9002 : ignoring unknown option '-std=c99'
pairlist.c
pairlist.c: warning C4819: The file contains a character that cannot be represented in the current code page (936). Save the file in Unicode format to prevent data loss
pairlist.c(106): error C2057: expected constant expression
pairlist.c(106): error C2466: cannot allocate an array of constant size 0
pairlist.c(106): error C2133: 'nResidents': unknown size
pairlist.c(114): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(122): error C2057: expected constant expression
pairlist.c(122): error C2466: cannot allocate an array of constant size 0
pairlist.c(122): error C2133: 'residents': unknown size
pairlist.c(123): error C2057: expected constant expression
pairlist.c(123): error C2466: cannot allocate an array of constant size 0
pairlist.c(123): error C2133: 'heads': unknown size
pairlist.c(124): error C2057: expected constant expression
pairlist.c(124): error C2466: cannot allocate an array of constant size 0
pairlist.c(124): error C2133: 'pointer': unknown size
pairlist.c(137): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(245): error C2057: expected constant expression
pairlist.c(245): error C2466: cannot allocate an array of constant size 0
pairlist.c(245): error C2133: 'nResidents0': unknown size
pairlist.c(246): error C2057: expected constant expression
pairlist.c(246): error C2466: cannot allocate an array of constant size 0
pairlist.c(246): error C2133: 'nResidents1': unknown size
pairlist.c(256): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(268): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(279): error C2057: expected constant expression
pairlist.c(279): error C2466: cannot allocate an array of constant size 0
pairlist.c(279): error C2133: 'pointer': unknown size
pairlist.c(282): error C2057: expected constant expression
pairlist.c(282): error C2466: cannot allocate an array of constant size 0
pairlist.c(282): error C2133: 'residents0': unknown size
pairlist.c(283): error C2057: expected constant expression
pairlist.c(283): error C2466: cannot allocate an array of constant size 0
pairlist.c(283): error C2133: 'heads0': unknown size
pairlist.c(297): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
pairlist.c(303): error C2057: expected constant expression
pairlist.c(303): error C2466: cannot allocate an array of constant size 0
pairlist.c(303): error C2133: 'residents1': unknown size
pairlist.c(304): error C2057: expected constant expression
pairlist.c(304): error C2466: cannot allocate an array of constant size 0
pairlist.c(304): error C2133: 'heads1': unknown size
pairlist.c(321): warning C4244: '=': conversion from 'double' to 'int', possible loss of data
error: Command "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\x86_amd64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Id:\ana\envs\python35\lib\site-packages\numpy\core\include -Id:\ana\envs\python35\include -Id:\ana\envs\python35\include -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" /Tcpairlist.c /Fobuild\temp.win-amd64-3.5\Release\pairlist.obj -std=c99" failed with exit status 2
----------------------------------------
ERROR: Command errored out with exit status 1: 'd:\ana\envs\python35\python.exe' -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\ADMINI~~1\AppData\Local\Temp\pip-install-k93z0ykf\pairlist\setup.py'"'"'; file='"'"'C:\Users\ADMINI~~1\AppData\Local\Temp\pip-install-k93z0ykf\pairlist\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record 'C:\Users\ADMINI~1\AppData\Local\Temp\pip-record-2s0kfk7e\install-record.txt' --single-version-externally-managed --compile --install-headers 'd:\ana\envs\python35\Include\pairlist' Check the logs for full command output.

Is it possible to add the generation of ice XIV in GenIce2?

I‘m using GenIce2 to generate structure files for a series of ice, and it has been very helpful for my work. Now I also need to generate structures for ice XIV. Could support for ice XIV be added to GenIce2?

Many thanks to this useful tool!

Installation of GenIce- windows

I am trying to install the GenIce package to python in windows using the pip3 install genice2 but it fails. here is the error message: (can you please assist). Many Thanks.

Collecting genice2
Using cached GenIce2-2.1.7-py2.py3-none-any.whl
Requirement already satisfied: yaplotlib>=0.1 in c:\users\100047903\appdata\local\packages\pythonsoftwarefoundation.python.3.10_qbz5n2kfra8p0\localcache\local-packages\python310\site-packages (from genice2) (0.1.2)
Requirement already satisfied: wheel in c:\users\100047903\appdata\local\packages\pythonsoftwarefoundation.python.3.10_qbz5n2kfra8p0\localcache\local-packages\python310\site-packages (from genice2) (0.40.0)
Collecting cycless
Using cached cycless-0.2-py2.py3-none-any.whl (9.3 kB)
Collecting pairlist>=0.2.12.4
Using cached PairList-0.2.12.4.tar.gz (10 kB)
Preparing metadata (setup.py) ... done
Collecting networkx>=2.0.dev20160901144005
Using cached networkx-3.0-py3-none-any.whl (2.0 MB)
Requirement already satisfied: numpy in c:\users\100047903\appdata\local\packages\pythonsoftwarefoundation.python.3.10_qbz5n2kfra8p0\localcache\local-packages\python310\site-packages (from genice2) (1.24.2)
Collecting openpyscad
Using cached openpyscad-0.5.0-py3-none-any.whl (9.7 kB)
Collecting tilecycles>=0.1.5.6
Using cached TileCycles-0.1.5.6-py3-none-any.whl
Collecting graphstat
Using cached graphstat-0.2.1-py2.py3-none-any.whl (3.9 kB)
Collecting methodtools
Using cached methodtools-0.4.7-py3-none-any.whl
Requirement already satisfied: six<2.0.0,>=1.14.0 in c:\users\100047903\appdata\local\packages\pythonsoftwarefoundation.python.3.10_qbz5n2kfra8p0\localcache\local-packages\python310\site-packages (from openpyscad->genice2) (1.16.0)
Collecting wirerope>=0.4.7
Using cached wirerope-0.4.7-py3-none-any.whl
Building wheels for collected packages: pairlist
Building wheel for pairlist (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [23 lines of output]
C:\Users\100047903\AppData\Local\Temp\pip-install-2b8vdyuj\pairlist_633079f7f84d47268f3d5d8b5cc75e0a\setup.py:4: DeprecationWarning:

    `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
    of the deprecation of `distutils` itself. It will be removed for
    Python >= 3.12. For older Python versions it will remain present.
    It is recommended to use `setuptools < 60.0` for those Python versions.
    For more details, see:
      https://numpy.org/devdocs/reference/distutils_status_migration.html


    from numpy.distutils.misc_util import get_numpy_include_dirs
  C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.2800.0_x64__qbz5n2kfra8p0\lib\site-packages\setuptools\dist.py:771: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
    warnings.warn(
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-cpython-310
  copying pairlist.py -> build\lib.win-amd64-cpython-310
  running build_ext
  INFO: No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
  building 'cpairlist' extension
  error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pairlist
Running setup.py clean for pairlist
Failed to build pairlist
Installing collected packages: wirerope, pairlist, openpyscad, networkx, methodtools, graphstat, cycless, tilecycles, genice2
Running setup.py install for pairlist ... error
error: subprocess-exited-with-error

× Running setup.py install for pairlist did not run successfully.
│ exit code: 1
╰─> [25 lines of output]
C:\Users\100047903\AppData\Local\Temp\pip-install-2b8vdyuj\pairlist_633079f7f84d47268f3d5d8b5cc75e0a\setup.py:4: DeprecationWarning:

    `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
    of the deprecation of `distutils` itself. It will be removed for
    Python >= 3.12. For older Python versions it will remain present.
    It is recommended to use `setuptools < 60.0` for those Python versions.
    For more details, see:
      https://numpy.org/devdocs/reference/distutils_status_migration.html


    from numpy.distutils.misc_util import get_numpy_include_dirs
  C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.2800.0_x64__qbz5n2kfra8p0\lib\site-packages\setuptools\dist.py:771: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
    warnings.warn(
  running install
  C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.2800.0_x64__qbz5n2kfra8p0\lib\site-packages\setuptools\command\install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
    warnings.warn(
  running build
  running build_py
  creating build
  creating build\lib.win-amd64-cpython-310
  copying pairlist.py -> build\lib.win-amd64-cpython-310
  running build_ext
  INFO: No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
  building 'cpairlist' extension
  error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> pairlist

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.

Is it possible to avoid printing extra comment lines at the end of .gro file?

Currently genice2 prints two extra lines at the end of .gro outputs. For example:
genice2 --water tip4p --rep 1 1 1 1h > test.gro
the content of test.gro is:

Generated by GenIce https://github.com/vitroid/GenIce 
64
    1ICE     OW    1   0.127   0.183   0.337
    1ICE    HW1    2   0.175   0.149   0.261
    1ICE    HW2    3   0.175   0.149   0.413
    1ICE     MW    4   0.139   0.175   0.337
    2ICE     OW    5   0.528   0.447   0.106
    2ICE    HW1    6   0.570   0.481   0.185
    2ICE    HW2    7   0.438   0.482   0.109
    2ICE     MW    8   0.522   0.456   0.117
    3ICE     OW    9   0.659   0.539   0.331
    3ICE    HW1   10   0.656   0.634   0.334
    3ICE    HW2   11   0.613   0.510   0.410
    3ICE     MW   12   0.652   0.547   0.341
    4ICE     OW   13   0.528   0.449   0.556
    4ICE    HW1   14   0.438   0.484   0.560
    4ICE    HW2   15   0.570   0.483   0.636
    4ICE     MW   16   0.522   0.458   0.567
    5ICE     OW   17   0.256   0.091   0.563
    5ICE    HW1   18   0.261  -0.004   0.562
    5ICE    HW2   19   0.348   0.119   0.562
    5ICE     MW   20   0.268   0.083   0.563
    6ICE     OW   21   0.271   0.551   0.561
    6ICE    HW1   22   0.223   0.518   0.636
    6ICE    HW2   23   0.223   0.517   0.485
    6ICE     MW   24   0.259   0.542   0.561
    7ICE     OW   25   0.520   0.171   0.116
    7ICE    HW1   26   0.522   0.267   0.113
    7ICE    HW2   27   0.565   0.143   0.037
    7ICE     MW   28   0.526   0.180   0.106
    8ICE     OW   29   0.520   0.173   0.567
    8ICE    HW1   30   0.565   0.144   0.488
    8ICE    HW2   31   0.523   0.269   0.563
    8ICE     MW   32   0.526   0.182   0.556
    9ICE     OW   33   0.140   0.461   0.786
    9ICE    HW1   34   0.137   0.365   0.787
    9ICE    HW2   35   0.049   0.489   0.786
    9ICE     MW   36   0.128   0.452   0.786
   10ICE     OW   37   0.140   0.459   0.336
   10ICE    HW1   38   0.049   0.487   0.336
   10ICE    HW2   39   0.137   0.364   0.336
   10ICE     MW   40   0.128   0.451   0.336
   11ICE     OW   41   0.271   0.549   0.110
   11ICE    HW1   42   0.223   0.516   0.186
   11ICE    HW2   43   0.223   0.516   0.034
   11ICE     MW   44   0.259   0.540   0.110
   12ICE     OW   45   0.256   0.089   0.112
   12ICE    HW1   46   0.261  -0.006   0.111
   12ICE    HW2   47   0.348   0.118   0.112
   12ICE     MW   48   0.268   0.081   0.112
   13ICE     OW   49   0.649   0.079   0.342
   13ICE    HW1   50   0.738   0.114   0.339
   13ICE    HW2   51   0.607   0.113   0.263
   13ICE     MW   52   0.655   0.088   0.331
   14ICE     OW   53   0.649   0.081   0.792
   14ICE    HW1   54   0.607   0.115   0.713
   14ICE    HW2   55   0.738   0.116   0.789
   14ICE     MW   56   0.655   0.090   0.782
   15ICE     OW   57   0.659   0.541   0.781
   15ICE    HW1   58   0.655   0.636   0.785
   15ICE    HW2   59   0.613   0.512   0.860
   15ICE     MW   60   0.652   0.549   0.792
   16ICE     OW   61   0.127   0.185   0.787
   16ICE    HW1   62   0.174   0.150   0.863
   16ICE    HW2   63   0.175   0.151   0.712
   16ICE     MW   64   0.139   0.176   0.787
    0.78228388 0.73535726 0.90365185
#
#Command line: c:\users\username\appdata\local\programs\python\python38\scripts\genice2 --water tip4p --rep 1 1 1 1h

The two extra lines at the end breaks some tools, such as trjconv coming from Gromacs itself:

> gmx -quiet trjconv -f .\test.gro
Note that major changes are planned in future for trjconv, to improve usability and utility.
Will write xtc: Compressed trajectory (portable xdr format): xtc
Reading frames from gro file 'Generated by GenIce https://github.com/vitroid/GenIce ', 64 atoms.
Reading frame       0 time    0.000   Reading frames from gro file 'Generated by GenIce https://github.com/vitroid/GenIce ', 64 atoms.
Reading frame       0 time    0.000
Precision of .\test.gro is 0.001 (nm)
Using output precision of 0.001 (nm)
 ->  frame      0 time    0.000
-------------------------------------------------------
Program:     gmx trjconv, version 2020.6-MODIFIED
Source file: src\gromacs\fileio\groio.cpp (line 67)

Fatal error:
gro file does not have the number of atoms on the second line

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Deleting the two extra lines fix the issue.
Of course I can always delete them manually, but that is a bit annoying :(

Ice XI

Hello,

I am attempting to generate a few Ice XI configurations (out of the 16 candidates) however the only 'type' option for ferroelectric Ice XI is '11i' which only provides me with one of the sixteen candidates for Ice XI. I am wondering if there is a way for me to specify which of the 16 candidates I would like. Any help would be greatly appreciated.

Missing guest molecules in filled ices

Hi,

I would like to generate filled ices with the code (especially the filled ice Ih structure) and it seems to me that the filled ices (C0, C1, C2, STprime) miss the guest molecule's cages in the code.

I was wondering if the cages of the filled ices and the filled ice Ih structure could be added.

Thank you very much.
Best wishes,
Eszter

Unsuccessful installation, numpy version issue

Hello, I'm trying to install genice2 in a newly created conda environment. I first installed all dependent packages via pip3, then installed genice2, but it seems that genice2 cannot run.

Please see my pip3 list:
(genice) raymond@pop-os:~$ pip3 list
Package Version

certifi 2021.5.30
cycless 0.1.4
decorator 4.4.2
GenIce2 2.1.1
graphstat 0.2.1
methodtools 0.4.3
networkx 2.5.1
numpy 1.19.3
openpyscad 0.5.0
PairList 0.2.11.1
pip 21.1.2
setuptools 52.0.0.post20210125
six 1.16.0
TileCycles 0.1.5.2
wheel 0.36.2
wirerope 0.4.3
yaplotlib 0.1.2

After I run "genice2 -h" or "genice2 --version", I got:
(genice) raymond@pop-os:~$ genice2 --version
RuntimeError: module compiled against API version 0xe but this version of numpy is 0xd
Traceback (most recent call last):
File "/home/raymond/miniconda3/envs/genice/bin/genice2", line 5, in
from genice2.cli.genice import main
File "/home/raymond/miniconda3/envs/genice/lib/python3.9/site-packages/genice2/cli/genice.py", line 8, in
from genice2.genice import GenIce
File "/home/raymond/miniconda3/envs/genice/lib/python3.9/site-packages/genice2/genice.py", line 16, in
import pairlist as pl
File "/home/raymond/miniconda3/envs/genice/lib/python3.9/site-packages/pairlist.py", line 10, in
from cpairlist import pairs, pairs2
ImportError: numpy.core.multiarray failed to import

My conda list is:
(genice) raymond@pop-os:~$ conda list
# packages in environment at /home/raymond/miniconda3/envs/genice:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
ca-certificates 2021.5.25 h06a4308_1
certifi 2021.5.30 py39h06a4308_0
cycless 0.1.4 pypi_0 pypi
decorator 4.4.2 pypi_0 pypi
genice2 2.1.1 pypi_0 pypi
graphstat 0.2.1 pypi_0 pypi
ld_impl_linux-64 2.35.1 h7274673_9
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgomp 9.3.0 h5101ec6_17
libstdcxx-ng 9.3.0 hd4cf53a_17
methodtools 0.4.3 pypi_0 pypi
ncurses 6.2 he6710b0_1
networkx 2.5.1 pypi_0 pypi
numpy 1.19.3 pypi_0 pypi
openpyscad 0.5.0 pypi_0 pypi
openssl 1.1.1k h27cfd23_0
pairlist 0.2.11.1 pypi_0 pypi
pip 21.1.2 py39h06a4308_0
python 3.9.5 h12debd9_4
readline 8.1 h27cfd23_0
setuptools 52.0.0 py39h06a4308_0
six 1.16.0 pypi_0 pypi
sqlite 3.35.4 hdfb4753_0
tilecycles 0.1.5.2 pypi_0 pypi
tk 8.6.10 hbc83047_0
tzdata 2021a h52ac0ba_0
wheel 0.36.2 pyhd3eb1b0_0
wirerope 0.4.3 pypi_0 pypi
xz 5.2.5 h7b6447c_0
yaplotlib 0.1.2 pypi_0 pypi
zlib 1.2.11 h7b6447c_3

Then I uninstalled the numpy1.19.3 and installed numpy 1.21.0 instead, it seems to work now.