Bulk Water¶
Set up environment (optional)¶
These steps are required for Google Colab, but may work on other systems too:
[1]:
#import locale
#locale.getpreferredencoding = lambda: "UTF-8"
#!python3 -m pip install pack-mm data-tutorials weas-widget
Let us start by creating a small box of water 10 A in size, for normal density that means 33 water molecules.
[2]:
from pack_mm.core.core import pack_molecules
from weas_widget import WeasWidget
e, final = pack_molecules(
molecule="H2O",
nmols=33,
arch="mace_mp",
model="small-0b2",
device="cpu",
where="anywhere",
cell_a=10,
cell_b=10,
cell_c=10,
seed=2025,
temperature=300,
ntries=20,
geometry=True,
threshold=0.5,
)
Inserting 33 H2O molecules in .
Using mace_mp model small-0b2 on cpu.
Insert in anywhere.
/home/runner/work/pack-mm/pack-mm/.venv/lib/python3.12/site-packages/e3nn/o3/_wigner.py:10: UserWarning: Environment variable TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD detected, since the`weights_only` argument was not explicitly passed to `torch.load`, forcing weights_only=False.
_Jd, _W3j_flat, _W3j_indices = torch.load(os.path.join(os.path.dirname(__file__), 'constants.pt'))
cuequivariance or cuequivariance_torch is not available. Cuequivariance acceleration will be disabled.
Using Materials Project MACE for MACECalculator with /home/runner/.cache/mace/macesmalldensityagnesistressmodel
Using float64 for MACECalculator, which is slower but more accurate. Recommended for geometry optimization.
Using head default out of ['default']
/home/runner/work/pack-mm/pack-mm/.venv/lib/python3.12/site-packages/mace/calculators/mace.py:143: UserWarning: Environment variable TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD detected, since the`weights_only` argument was not explicitly passed to `torch.load`, forcing weights_only=False.
torch.load(f=model_path, map_location=device)
Old energy=0.0, new energy=-14.169908427446725, de=-14.169908427446725, acc=1.106790443611292e+238, random=0.6573675854710377
Inserted particle 1
Old energy=-14.169908427446725, new energy=-28.388449306260235, de=-14.21854087881351, acc=7.261977566080532e+238, random=0.7694578719378116
Inserted particle 2
Old energy=-28.388449306260235, new energy=-42.56138109854783, de=-14.172931792287592, acc=1.2441012080374936e+238, random=0.6663921049033288
Inserted particle 3
Old energy=-42.56138109854783, new energy=-56.72045170438421, de=-14.159070605836384, acc=7.277763676747897e+237, random=0.5196536887579605
Inserted particle 4
Old energy=-56.72045170438421, new energy=-70.95493496595596, de=-14.234483261571746, acc=1.345473773274851e+239, random=0.06739574665921966
Inserted particle 5
Old energy=-70.95493496595596, new energy=-85.20119759619391, de=-14.24626263023795, acc=2.122071379141933e+239, random=0.49961201043327175
Inserted particle 6
Old energy=-85.20119759619391, new energy=-99.4226181862961, de=-14.221420590102198, acc=8.117680232384532e+238, random=0.1050746012583641
Inserted particle 7
Old energy=-99.4226181862961, new energy=-113.79662130272759, de=-14.374003116431481, acc=2.9696579904155567e+241, random=0.9378701885604214
Inserted particle 8
Old energy=-113.79662130272759, new energy=-128.1306220375978, de=-14.334000734870202, acc=6.319689981828159e+240, random=0.3762683149324123
Inserted particle 9
Old energy=-128.1306220375978, new energy=-141.85615337199786, de=-13.725531334400074, acc=3.7918946959024316e+230, random=0.6727933834766038
Inserted particle 10
Old energy=-141.85615337199786, new energy=-156.06180658142108, de=-14.205653209423218, acc=4.411146815908922e+238, random=0.09706066849775918
Inserted particle 11
Old energy=-156.06180658142108, new energy=-170.53713931561308, de=-14.475332734191994, acc=1.4961311672716866e+243, random=0.47590567428965436
Inserted particle 12
Old energy=-170.53713931561308, new energy=-184.44423715363098, de=-13.907097838017904, acc=4.256379248320164e+233, random=0.1445197281328413
Inserted particle 13
Old energy=-184.44423715363098, new energy=-198.8723316569115, de=-14.428094503280533, acc=2.40658967246052e+242, random=0.6096984257895941
Inserted particle 14
Old energy=-198.8723316569115, new energy=-213.0472463472201, de=-14.174914690308583, acc=1.3432812220838868e+238, random=0.10084644599814097
Inserted particle 15
Old energy=-213.0472463472201, new energy=-225.548543930126, de=-12.501297582905892, acc=1.0295025792391397e+210, random=0.8475810108898351
Inserted particle 16
Old energy=-225.548543930126, new energy=-237.81867754510063, de=-12.27013361497464, acc=1.3466116834684025e+206, random=0.9573928760728474
Inserted particle 17
Old energy=-237.81867754510063, new energy=-251.69716390805326, de=-13.878486362952628, acc=1.4073059625944881e+233, random=0.3273810695294246
Inserted particle 18
Old energy=-251.69716390805326, new energy=-240.75598269219518, de=10.94118121585808, acc=1.571024294231746e-184, random=0.06247404096988407
Old energy=-251.69716390805326, new energy=-265.98484303063964, de=-14.287679122586383, acc=1.0532383716582671e+240, random=0.9267631049637567
Inserted particle 19
Old energy=-265.98484303063964, new energy=-273.78462117763786, de=-7.7997781469982215, acc=1.07287796861951e+131, random=0.3402871935608006
Inserted particle 20
Old energy=-273.78462117763786, new energy=-285.09649060859454, de=-11.311869430956676, acc=1.0742544121330106e+190, random=0.1776678297264329
Inserted particle 21
Old energy=-285.09649060859454, new energy=-298.76729278681404, de=-13.670802178219503, acc=4.5650611352144245e+229, random=0.6002380235886438
Inserted particle 22
Old energy=-298.76729278681404, new energy=-286.0973160835177, de=12.669976703296356, acc=1.4245808268246304e-213, random=0.868138468423006
Old energy=-298.76729278681404, new energy=-312.42081274657045, de=-13.653519959756409, acc=2.339472838800911e+229, random=0.657014836768514
Inserted particle 23
Old energy=-312.42081274657045, new energy=-315.2519351263058, de=-2.8311223797353477, acc=3.63729764384701e+47, random=0.5318473353823712
Old energy=-312.42081274657045, new energy=-324.38286676790995, de=-11.962054021339497, acc=8.989410999140108e+200, random=0.9616436876719956
Inserted particle 24
Old energy=-324.38286676790995, new energy=-334.7276976756465, de=-10.344830907736537, acc=6.103366546753475e+173, random=0.21200357006485315
Inserted particle 25
Old energy=-334.7276976756465, new energy=-348.8852358657079, de=-14.157538190061416, acc=6.85890027328025e+237, random=0.4817459907937399
Inserted particle 26
Old energy=-348.8852358657079, new energy=-360.3771726445383, de=-11.491936778830393, acc=1.1379062387491906e+193, random=0.7175118692379753
Inserted particle 27
Old energy=-360.3771726445383, new energy=-370.71946686737834, de=-10.342294222840053, acc=5.532927860100863e+173, random=0.4094954707153864
Inserted particle 28
Old energy=-370.71946686737834, new energy=-381.90781888174286, de=-11.188352014364511, acc=9.038683297493437e+187, random=0.19004083637014857
Inserted particle 29
Old energy=-381.90781888174286, new energy=-390.1891332215735, de=-8.281314339830658, acc=1.3182721379968262e+139, random=0.2593074228409512
Inserted particle 30
Old energy=-390.1891332215735, new energy=-392.71942108765535, de=-2.530287866081835, acc=3.2135105364186836e+42, random=0.368706041406911
Old energy=-390.1891332215735, new energy=-343.227703525221, de=46.961429696352525, acc=0.0, random=0.29948735641057544
Old energy=-390.1891332215735, new energy=-391.94706464719314, de=-1.7579314256196312, acc=3.403754206189546e+29, random=0.11024899776641639
Old energy=-390.1891332215735, new energy=-397.4714077514512, de=-7.282274529877668, acc=2.1720471159563655e+122, random=0.853089891818317
Inserted particle 31
Old energy=-397.4714077514512, new energy=-201.84842710657364, de=195.62298064487754, acc=0.0, random=0.7172312048224184
Old energy=-397.4714077514512, new energy=-409.51758859289333, de=-12.046180841442151, acc=2.328091753685072e+202, random=0.7007421832233066
Inserted particle 32
Old energy=-409.51758859289333, new energy=-422.30745403223574, de=-12.789865439342407, acc=7.250295553039641e+214, random=0.37954479237838723
Inserted particle 33
Using Materials Project MACE for MACECalculator with /home/runner/.cache/mace/macesmalldensityagnesistressmodel
Using float64 for MACECalculator, which is slower but more accurate. Recommended for geometry optimization.
Using head default out of ['default']
/home/runner/work/pack-mm/pack-mm/.venv/lib/python3.12/site-packages/mace/calculators/mace.py:143: UserWarning: Environment variable TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD detected, since the`weights_only` argument was not explicitly passed to `torch.load`, forcing weights_only=False.
torch.load(f=model_path, map_location=device)
Step Time Energy fmax
LBFGS: 0 10:03:49 -422.307454 13.877663
LBFGS: 1 10:03:49 -435.791603 15.542238
LBFGS: 2 10:03:50 -445.636460 8.628340
LBFGS: 3 10:03:51 -451.808973 4.176232
LBFGS: 4 10:03:51 -455.545885 3.666724
LBFGS: 5 10:03:52 -458.932705 3.087802
LBFGS: 6 10:03:53 -462.238560 2.496349
LBFGS: 7 10:03:53 -464.286151 3.489929
LBFGS: 8 10:03:54 -466.032275 2.215424
LBFGS: 9 10:03:55 -467.425347 1.697507
LBFGS: 10 10:03:55 -468.662562 2.029074
LBFGS: 11 10:03:56 -469.699687 2.413723
LBFGS: 12 10:03:57 -470.733457 1.752417
LBFGS: 13 10:03:57 -471.567068 1.079853
LBFGS: 14 10:03:58 -472.669489 1.711636
LBFGS: 15 10:03:58 -473.205563 1.634225
LBFGS: 16 10:03:59 -473.831545 1.175250
LBFGS: 17 10:04:00 -474.157829 2.514301
LBFGS: 18 10:04:00 -474.720307 1.106639
LBFGS: 19 10:04:01 -475.243021 0.929779
LBFGS: 20 10:04:02 -475.673385 1.057766
LBFGS: 21 10:04:02 -475.932370 0.881880
LBFGS: 22 10:04:03 -476.175535 0.882676
LBFGS: 23 10:04:04 -476.420049 1.188850
LBFGS: 24 10:04:04 -476.594292 0.765145
LBFGS: 25 10:04:05 -476.862982 0.805157
LBFGS: 26 10:04:05 -477.133243 0.879516
LBFGS: 27 10:04:06 -477.358436 1.161428
LBFGS: 28 10:04:07 -477.583134 0.853986
LBFGS: 29 10:04:07 -477.816074 0.892980
LBFGS: 30 10:04:08 -478.002069 0.802879
LBFGS: 31 10:04:08 -478.159765 0.907363
LBFGS: 32 10:04:09 -478.304739 0.732561
LBFGS: 33 10:04:10 -478.516317 0.698569
LBFGS: 34 10:04:10 -478.721229 0.788372
LBFGS: 35 10:04:11 -478.936063 0.775582
LBFGS: 36 10:04:11 -479.103873 0.650802
LBFGS: 37 10:04:12 -479.262580 0.675939
LBFGS: 38 10:04:13 -479.421737 0.860773
LBFGS: 39 10:04:13 -479.601171 0.640421
LBFGS: 40 10:04:14 -479.790530 0.622390
LBFGS: 41 10:04:15 -479.910151 0.659465
LBFGS: 42 10:04:15 -480.006815 0.481454
LBFGS: 43 10:04:16 -480.136074 0.590734
LBFGS: 44 10:04:17 -480.262922 0.953696
LBFGS: 45 10:04:17 -480.392769 0.508664
LBFGS: 46 10:04:18 -480.490737 0.586978
LBFGS: 47 10:04:18 -480.588302 0.639654
LBFGS: 48 10:04:19 -480.763744 0.638177
LBFGS: 49 10:04:20 -480.897251 0.534118
LBFGS: 50 10:04:20 -481.021311 0.485723
LBFGS: 51 10:04:21 -481.127862 0.582302
LBFGS: 52 10:04:22 -481.232738 0.612588
LBFGS: 53 10:04:22 -481.347576 0.649466
LBFGS: 54 10:04:23 -481.454183 0.629958
LBFGS: 55 10:04:24 -481.556168 0.408971
LBFGS: 56 10:04:24 -481.641221 0.448516
LBFGS: 57 10:04:25 -481.724783 0.448668
LBFGS: 58 10:04:25 -481.835808 0.413646
LBFGS: 59 10:04:26 -481.914032 0.685601
LBFGS: 60 10:04:27 -481.981834 0.460009
LBFGS: 61 10:04:27 -482.056799 0.391624
LBFGS: 62 10:04:28 -482.132678 0.308693
LBFGS: 63 10:04:29 -482.215704 0.362441
LBFGS: 64 10:04:29 -482.271780 0.359791
LBFGS: 65 10:04:30 -482.338623 0.381272
LBFGS: 66 10:04:31 -482.395852 0.422197
LBFGS: 67 10:04:31 -482.458444 0.386613
LBFGS: 68 10:04:32 -482.532481 0.394048
LBFGS: 69 10:04:32 -482.601371 0.402546
LBFGS: 70 10:04:33 -482.653404 0.353862
LBFGS: 71 10:04:33 -482.691509 0.377310
LBFGS: 72 10:04:34 -482.734611 0.330249
LBFGS: 73 10:04:35 -482.799811 0.381771
LBFGS: 74 10:04:35 -482.857080 0.447662
LBFGS: 75 10:04:36 -482.917838 0.376530
LBFGS: 76 10:04:36 -482.968576 0.315092
LBFGS: 77 10:04:37 -483.020101 0.310454
LBFGS: 78 10:04:38 -483.066142 0.347737
LBFGS: 79 10:04:38 -483.112253 0.311655
LBFGS: 80 10:04:39 -483.152855 0.330687
LBFGS: 81 10:04:40 -483.191872 0.268214
LBFGS: 82 10:04:40 -483.224914 0.444314
LBFGS: 83 10:04:41 -483.260812 0.273215
LBFGS: 84 10:04:41 -483.299696 0.464131
LBFGS: 85 10:04:42 -483.342284 0.301555
LBFGS: 86 10:04:43 -483.380349 0.306767
LBFGS: 87 10:04:43 -483.408996 0.324211
LBFGS: 88 10:04:44 -483.442423 0.342084
LBFGS: 89 10:04:45 -483.484117 0.290656
LBFGS: 90 10:04:45 -483.530734 0.297088
LBFGS: 91 10:04:46 -483.560967 0.248771
LBFGS: 92 10:04:46 -483.600029 0.496099
LBFGS: 93 10:04:47 -483.648500 0.461463
LBFGS: 94 10:04:48 -483.694032 0.991481
LBFGS: 95 10:04:48 -483.760075 0.537253
LBFGS: 96 10:04:49 -483.806151 0.382515
LBFGS: 97 10:04:50 -483.840036 0.343295
LBFGS: 98 10:04:50 -483.870776 0.350422
LBFGS: 99 10:04:51 -483.921631 0.429895
LBFGS: 100 10:04:52 -483.964606 0.493320
LBFGS: 101 10:04:52 -483.996736 0.413153
LBFGS: 102 10:04:53 -484.032976 0.290601
LBFGS: 103 10:04:54 -484.070603 0.287103
LBFGS: 104 10:04:54 -484.102650 0.266610
LBFGS: 105 10:04:55 -484.135817 0.265643
LBFGS: 106 10:04:56 -484.162171 0.250369
LBFGS: 107 10:04:56 -484.189260 0.292546
LBFGS: 108 10:04:57 -484.218740 0.307706
LBFGS: 109 10:04:57 -484.248908 0.565371
LBFGS: 110 10:04:58 -484.278317 0.251354
LBFGS: 111 10:04:59 -484.303058 0.216327
LBFGS: 112 10:04:59 -484.320560 0.222344
LBFGS: 113 10:05:00 -484.340146 0.220412
LBFGS: 114 10:05:00 -484.365009 0.237987
LBFGS: 115 10:05:01 -484.388229 0.175008
LBFGS: 116 10:05:02 -484.410060 0.206289
LBFGS: 117 10:05:02 -484.430236 0.204077
LBFGS: 118 10:05:03 -484.452477 0.252451
LBFGS: 119 10:05:04 -484.475909 0.273568
LBFGS: 120 10:05:04 -484.498683 0.301674
LBFGS: 121 10:05:05 -484.518715 0.308904
LBFGS: 122 10:05:06 -484.537707 0.230892
LBFGS: 123 10:05:06 -484.559027 0.203116
LBFGS: 124 10:05:07 -484.580842 0.256442
LBFGS: 125 10:05:07 -484.603562 0.279154
LBFGS: 126 10:05:08 -484.623792 0.214331
LBFGS: 127 10:05:09 -484.642449 0.210542
LBFGS: 128 10:05:10 -484.661975 0.295669
LBFGS: 129 10:05:10 -484.689154 0.401151
LBFGS: 130 10:05:11 -484.718332 0.308726
LBFGS: 131 10:05:11 -484.741818 0.382969
LBFGS: 132 10:05:12 -484.763953 0.216638
LBFGS: 133 10:05:13 -484.787856 0.235513
LBFGS: 134 10:05:13 -484.812531 0.264937
LBFGS: 135 10:05:14 -484.835766 0.402124
LBFGS: 136 10:05:15 -484.858430 0.217953
LBFGS: 137 10:05:15 -484.877321 0.179554
LBFGS: 138 10:05:16 -484.898387 0.261446
LBFGS: 139 10:05:17 -484.921435 0.243394
LBFGS: 140 10:05:17 -484.948703 0.319621
LBFGS: 141 10:05:18 -484.971011 0.261375
LBFGS: 142 10:05:18 -484.991352 0.230271
LBFGS: 143 10:05:19 -485.011476 0.211258
LBFGS: 144 10:05:19 -485.036650 0.291015
LBFGS: 145 10:05:20 -485.059316 0.183163
LBFGS: 146 10:05:21 -485.079177 0.199940
LBFGS: 147 10:05:21 -485.097575 0.197279
LBFGS: 148 10:05:22 -485.115220 0.225396
LBFGS: 149 10:05:23 -485.131850 0.206028
LBFGS: 150 10:05:23 -485.148505 0.180702
LBFGS: 151 10:05:24 -485.164133 0.192611
LBFGS: 152 10:05:25 -485.179739 0.192113
LBFGS: 153 10:05:25 -485.193961 0.157355
LBFGS: 154 10:05:26 -485.206883 0.150161
LBFGS: 155 10:05:26 -485.217582 0.131592
LBFGS: 156 10:05:27 -485.226837 0.132444
LBFGS: 157 10:05:28 -485.236188 0.135832
LBFGS: 158 10:05:28 -485.246934 0.128134
LBFGS: 159 10:05:29 -485.258847 0.150498
LBFGS: 160 10:05:30 -485.271095 0.170130
LBFGS: 161 10:05:30 -485.282843 0.206553
LBFGS: 162 10:05:31 -485.293838 0.155075
LBFGS: 163 10:05:32 -485.304935 0.155148
LBFGS: 164 10:05:32 -485.316105 0.131736
LBFGS: 165 10:05:33 -485.327063 0.189752
LBFGS: 166 10:05:34 -485.337150 0.153041
LBFGS: 167 10:05:34 -485.347754 0.150834
LBFGS: 168 10:05:35 -485.359310 0.153122
LBFGS: 169 10:05:35 -485.371676 0.162032
LBFGS: 170 10:05:36 -485.382159 0.141829
LBFGS: 171 10:05:37 -485.390717 0.119533
LBFGS: 172 10:05:37 -485.399287 0.143391
LBFGS: 173 10:05:38 -485.410824 0.179853
LBFGS: 174 10:05:39 -485.424947 0.205613
LBFGS: 175 10:05:39 -485.438451 0.241444
LBFGS: 176 10:05:40 -485.448004 0.214438
LBFGS: 177 10:05:41 -485.456397 0.134944
LBFGS: 178 10:05:41 -485.464157 0.134600
LBFGS: 179 10:05:42 -485.473787 0.186862
LBFGS: 180 10:05:42 -485.480682 0.173867
LBFGS: 181 10:05:43 -485.487156 0.115708
LBFGS: 182 10:05:44 -485.493831 0.128686
LBFGS: 183 10:05:44 -485.501392 0.116803
LBFGS: 184 10:05:45 -485.508188 0.154473
LBFGS: 185 10:05:46 -485.513987 0.102476
LBFGS: 186 10:05:46 -485.519603 0.105021
LBFGS: 187 10:05:47 -485.525997 0.152851
LBFGS: 188 10:05:48 -485.532837 0.173253
LBFGS: 189 10:05:48 -485.538829 0.115083
LBFGS: 190 10:05:49 -485.543717 0.090572
[3]:
viewer=WeasWidget()
viewer.from_ase(final)
viewer.avr.model_style = 1
viewer.avr.show_hydrogen_bonds = True
viewer
[3]:
[4]:
m = sum(final.get_masses())*1.660538921*10**(-24)
V = final.get_volume()*10**(-24)
rho = m/V
print(final.cell.cellpar())
print(f"Mass: {m:.3e} g")
print(f"Volume: {V:.3e} cm^3")
print(f"Density: {rho:.2f} g/cm^3")
[10.12960782 10.12960782 10.12960782 90. 90. 90. ]
Mass: 9.872e-22 g
Volume: 1.039e-21 cm^3
Density: 0.95 g/cm^3