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.
/home/runner/work/pack-mm/pack-mm/.venv/lib/python3.12/site-packages/mace/calculators/mace.py:199: 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=-14.169908427446723, de=-14.169908427446723, acc=np.float64(1.106790443611292e+238), random=0.6573675854710377
Inserted particle 1
Old energy=-14.169908427446723, new energy=-28.388449306260227, de=-14.218540878813505, acc=np.float64(7.261977566078882e+238), random=0.7694578719378116
Inserted particle 2
Old energy=-28.388449306260227, new energy=-42.56138109854783, de=-14.1729317922876, acc=np.float64(1.2441012080377765e+238), random=0.6663921049033288
Inserted particle 3
Old energy=-42.56138109854783, new energy=-56.7204517043842, de=-14.159070605836376, acc=np.float64(7.277763676746241e+237), random=0.5196536887579605
Inserted particle 4
Old energy=-56.7204517043842, new energy=-70.95493496595596, de=-14.234483261571754, acc=np.float64(1.3454737732753098e+239), random=0.06739574665921966
Inserted particle 5
Old energy=-70.95493496595596, new energy=-85.20119759619391, de=-14.24626263023795, acc=np.float64(2.122071379141933e+239), random=0.49961201043327175
Inserted particle 6
Old energy=-85.20119759619391, new energy=-99.42261818629609, de=-14.221420590102184, acc=np.float64(8.117680232379918e+238), random=0.1050746012583641
Inserted particle 7
Old energy=-99.42261818629609, new energy=-113.7966213027276, de=-14.37400311643151, acc=np.float64(2.9696579904185955e+241), random=0.9378701885604214
Inserted particle 8
Old energy=-113.7966213027276, new energy=-128.1306220375978, de=-14.334000734870187, acc=np.float64(6.319689981824566e+240), random=0.3762683149324123
Inserted particle 9
Old energy=-128.1306220375978, new energy=-141.85615337199786, de=-13.725531334400074, acc=np.float64(3.7918946959024316e+230), random=0.6727933834766038
Inserted particle 10
Old energy=-141.85615337199786, new energy=-156.06180658142108, de=-14.205653209423218, acc=np.float64(4.411146815908922e+238), random=0.09706066849775918
Inserted particle 11
Old energy=-156.06180658142108, new energy=-170.53713931561308, de=-14.475332734191994, acc=np.float64(1.4961311672716866e+243), random=0.47590567428965436
Inserted particle 12
Old energy=-170.53713931561308, new energy=-184.44423715363098, de=-13.907097838017904, acc=np.float64(4.256379248320164e+233), random=0.1445197281328413
Inserted particle 13
Old energy=-184.44423715363098, new energy=-198.8723316569115, de=-14.428094503280533, acc=np.float64(2.40658967246052e+242), random=0.6096984257895941
Inserted particle 14
Old energy=-198.8723316569115, new energy=-213.04724634722004, de=-14.174914690308526, acc=np.float64(1.3432812220809855e+238), random=0.10084644599814097
Inserted particle 15
Old energy=-213.04724634722004, new energy=-225.548543930126, de=-12.501297582905949, acc=np.float64(1.0295025792414219e+210), random=0.8475810108898351
Inserted particle 16
Old energy=-225.548543930126, new energy=-237.81867754510063, de=-12.27013361497464, acc=np.float64(1.3466116834684025e+206), random=0.9573928760728474
Inserted particle 17
Old energy=-237.81867754510063, new energy=-251.6971639080533, de=-13.878486362952685, acc=np.float64(1.4073059625976879e+233), random=0.3273810695294246
Inserted particle 18
Old energy=-251.6971639080533, new energy=-240.75598269219518, de=10.941181215858137, acc=np.float64(1.5710242942282633e-184), random=0.06247404096988407
Old energy=-251.6971639080533, new energy=-265.98484303063964, de=-14.287679122586326, acc=np.float64(1.0532383716559922e+240), random=0.9267631049637567
Inserted particle 19
Old energy=-265.98484303063964, new energy=-273.78462117763786, de=-7.7997781469982215, acc=np.float64(1.07287796861951e+131), random=0.3402871935608006
Inserted particle 20
Old energy=-273.78462117763786, new energy=-285.0964906085945, de=-11.31186943095662, acc=np.float64(1.0742544121306291e+190), random=0.1776678297264329
Inserted particle 21
Old energy=-285.0964906085945, new energy=-298.767292786814, de=-13.670802178219503, acc=np.float64(4.5650611352144245e+229), random=0.6002380235886438
Inserted particle 22
Old energy=-298.767292786814, new energy=-286.0973160835176, de=12.669976703296356, acc=np.float64(1.4245808268246304e-213), random=0.868138468423006
Old energy=-298.767292786814, new energy=-312.4208127465705, de=-13.653519959756522, acc=np.float64(2.3394728388110177e+229), random=0.657014836768514
Inserted particle 23
Old energy=-312.4208127465705, new energy=-315.2519351263058, de=-2.831122379735291, acc=np.float64(3.63729764383905e+47), random=0.5318473353823712
Old energy=-312.4208127465705, new energy=-324.38286676790995, de=-11.96205402133944, acc=np.float64(8.98941099912018e+200), random=0.9616436876719956
Inserted particle 24
Old energy=-324.38286676790995, new energy=-334.7276976756465, de=-10.344830907736537, acc=np.float64(6.103366546753475e+173), random=0.21200357006485315
Inserted particle 25
Old energy=-334.7276976756465, new energy=-348.8852358657079, de=-14.157538190061416, acc=np.float64(6.85890027328025e+237), random=0.4817459907937399
Inserted particle 26
Old energy=-348.8852358657079, new energy=-360.3771726445383, de=-11.491936778830393, acc=np.float64(1.1379062387491906e+193), random=0.7175118692379753
Inserted particle 27
Old energy=-360.3771726445383, new energy=-370.71946686737834, de=-10.342294222840053, acc=np.float64(5.532927860100863e+173), random=0.4094954707153864
Inserted particle 28
Old energy=-370.71946686737834, new energy=-381.90781888174286, de=-11.188352014364511, acc=np.float64(9.038683297493437e+187), random=0.19004083637014857
Inserted particle 29
Old energy=-381.90781888174286, new energy=-390.1891332215734, de=-8.281314339830544, acc=np.float64(1.3182721379910562e+139), random=0.2593074228409512
Inserted particle 30
Old energy=-390.1891332215734, new energy=-392.71942108765535, de=-2.5302878660819488, acc=np.float64(3.213510536432795e+42), random=0.368706041406911
Old energy=-390.1891332215734, new energy=-343.2277035252214, de=46.96142969635201, acc=np.float64(0.0), random=0.29948735641057544
Old energy=-390.1891332215734, new energy=-391.9470646471931, de=-1.757931425619688, acc=np.float64(3.4037542061970436e+29), random=0.11024899776641639
Old energy=-390.1891332215734, new energy=-397.4714077514512, de=-7.282274529877782, acc=np.float64(2.1720471159658727e+122), random=0.853089891818317
Inserted particle 31
Old energy=-397.4714077514512, new energy=-201.84842710657355, de=195.62298064487763, acc=np.float64(0.0), random=0.7172312048224184
Old energy=-397.4714077514512, new energy=-409.5175885928934, de=-12.046180841442208, acc=np.float64(2.328091753690233e+202), random=0.7007421832233066
Inserted particle 32
Old energy=-409.5175885928934, new energy=-422.30745403223574, de=-12.78986543934235, acc=np.float64(7.250295553023568e+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.
/home/runner/work/pack-mm/pack-mm/.venv/lib/python3.12/site-packages/mace/calculators/mace.py:199: 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 19:01:11 -422.307454 13.877663
LBFGS: 1 19:01:12 -435.791603 15.542238
LBFGS: 2 19:01:12 -445.636460 8.628340
LBFGS: 3 19:01:13 -451.808973 4.176232
LBFGS: 4 19:01:13 -455.545885 3.666724
LBFGS: 5 19:01:14 -458.932705 3.087802
LBFGS: 6 19:01:14 -462.238560 2.496349
LBFGS: 7 19:01:15 -464.286151 3.489929
LBFGS: 8 19:01:15 -466.032275 2.215424
LBFGS: 9 19:01:15 -467.425347 1.697507
LBFGS: 10 19:01:16 -468.662562 2.029074
LBFGS: 11 19:01:16 -469.699687 2.413723
LBFGS: 12 19:01:17 -470.733457 1.752417
LBFGS: 13 19:01:17 -471.567068 1.079853
LBFGS: 14 19:01:18 -472.669489 1.711636
LBFGS: 15 19:01:18 -473.205563 1.634225
LBFGS: 16 19:01:19 -473.831545 1.175250
LBFGS: 17 19:01:19 -474.157829 2.514301
LBFGS: 18 19:01:20 -474.720307 1.106639
LBFGS: 19 19:01:20 -475.243021 0.929779
LBFGS: 20 19:01:21 -475.673385 1.057766
LBFGS: 21 19:01:21 -475.932370 0.881880
LBFGS: 22 19:01:22 -476.175535 0.882676
LBFGS: 23 19:01:22 -476.420049 1.188850
LBFGS: 24 19:01:23 -476.594292 0.765145
LBFGS: 25 19:01:23 -476.862982 0.805157
LBFGS: 26 19:01:23 -477.133243 0.879516
LBFGS: 27 19:01:24 -477.358436 1.161428
LBFGS: 28 19:01:24 -477.583134 0.853986
LBFGS: 29 19:01:25 -477.816074 0.892980
LBFGS: 30 19:01:25 -478.002069 0.802879
LBFGS: 31 19:01:26 -478.159765 0.907363
LBFGS: 32 19:01:26 -478.304739 0.732561
LBFGS: 33 19:01:27 -478.516317 0.698569
LBFGS: 34 19:01:27 -478.721229 0.788372
LBFGS: 35 19:01:28 -478.936063 0.775582
LBFGS: 36 19:01:28 -479.103873 0.650802
LBFGS: 37 19:01:29 -479.262580 0.675939
LBFGS: 38 19:01:29 -479.421737 0.860773
LBFGS: 39 19:01:30 -479.601171 0.640421
LBFGS: 40 19:01:30 -479.790530 0.622390
LBFGS: 41 19:01:31 -479.910151 0.659465
LBFGS: 42 19:01:31 -480.006815 0.481454
LBFGS: 43 19:01:31 -480.136074 0.590734
LBFGS: 44 19:01:32 -480.262922 0.953696
LBFGS: 45 19:01:32 -480.392769 0.508664
LBFGS: 46 19:01:33 -480.490737 0.586978
LBFGS: 47 19:01:33 -480.588302 0.639654
LBFGS: 48 19:01:34 -480.763744 0.638177
LBFGS: 49 19:01:34 -480.897251 0.534118
LBFGS: 50 19:01:35 -481.021311 0.485723
LBFGS: 51 19:01:35 -481.127862 0.582302
LBFGS: 52 19:01:36 -481.232738 0.612588
LBFGS: 53 19:01:36 -481.347576 0.649466
LBFGS: 54 19:01:37 -481.454183 0.629958
LBFGS: 55 19:01:37 -481.556168 0.408971
LBFGS: 56 19:01:37 -481.641221 0.448516
LBFGS: 57 19:01:38 -481.724783 0.448668
LBFGS: 58 19:01:38 -481.835808 0.413646
LBFGS: 59 19:01:39 -481.914032 0.685601
LBFGS: 60 19:01:39 -481.981834 0.460009
LBFGS: 61 19:01:40 -482.056799 0.391624
LBFGS: 62 19:01:40 -482.132678 0.308693
LBFGS: 63 19:01:41 -482.215704 0.362441
LBFGS: 64 19:01:41 -482.271780 0.359791
LBFGS: 65 19:01:42 -482.338623 0.381272
LBFGS: 66 19:01:42 -482.395852 0.422197
LBFGS: 67 19:01:43 -482.458444 0.386613
LBFGS: 68 19:01:43 -482.532481 0.394048
LBFGS: 69 19:01:44 -482.601371 0.402546
LBFGS: 70 19:01:44 -482.653404 0.353862
LBFGS: 71 19:01:45 -482.691509 0.377310
LBFGS: 72 19:01:45 -482.734611 0.330249
LBFGS: 73 19:01:45 -482.799811 0.381771
LBFGS: 74 19:01:46 -482.857080 0.447662
LBFGS: 75 19:01:46 -482.917838 0.376530
LBFGS: 76 19:01:47 -482.968576 0.315092
LBFGS: 77 19:01:47 -483.020101 0.310454
LBFGS: 78 19:01:48 -483.066142 0.347737
LBFGS: 79 19:01:48 -483.112253 0.311655
LBFGS: 80 19:01:49 -483.152855 0.330687
LBFGS: 81 19:01:49 -483.191872 0.268214
LBFGS: 82 19:01:50 -483.224914 0.444314
LBFGS: 83 19:01:50 -483.260812 0.273215
LBFGS: 84 19:01:51 -483.299696 0.464131
LBFGS: 85 19:01:51 -483.342284 0.301555
LBFGS: 86 19:01:52 -483.380349 0.306767
LBFGS: 87 19:01:52 -483.408996 0.324211
LBFGS: 88 19:01:52 -483.442423 0.342084
LBFGS: 89 19:01:53 -483.484117 0.290656
LBFGS: 90 19:01:53 -483.530734 0.297088
LBFGS: 91 19:01:54 -483.560967 0.248771
LBFGS: 92 19:01:54 -483.600029 0.496099
LBFGS: 93 19:01:55 -483.648500 0.461463
LBFGS: 94 19:01:55 -483.694032 0.991481
LBFGS: 95 19:01:56 -483.760075 0.537253
LBFGS: 96 19:01:56 -483.806151 0.382515
LBFGS: 97 19:01:57 -483.840036 0.343295
LBFGS: 98 19:01:57 -483.870776 0.350422
LBFGS: 99 19:01:58 -483.921631 0.429895
LBFGS: 100 19:01:58 -483.964606 0.493320
LBFGS: 101 19:01:58 -483.996736 0.413153
LBFGS: 102 19:01:59 -484.032976 0.290601
LBFGS: 103 19:01:59 -484.070603 0.287103
LBFGS: 104 19:02:00 -484.102650 0.266610
LBFGS: 105 19:02:00 -484.135817 0.265643
LBFGS: 106 19:02:01 -484.162171 0.250369
LBFGS: 107 19:02:01 -484.189260 0.292546
LBFGS: 108 19:02:02 -484.218740 0.307706
LBFGS: 109 19:02:02 -484.248908 0.565371
LBFGS: 110 19:02:03 -484.278317 0.251354
LBFGS: 111 19:02:03 -484.303058 0.216327
LBFGS: 112 19:02:04 -484.320560 0.222344
LBFGS: 113 19:02:04 -484.340146 0.220412
LBFGS: 114 19:02:05 -484.365009 0.237987
LBFGS: 115 19:02:05 -484.388229 0.175008
LBFGS: 116 19:02:05 -484.410060 0.206289
LBFGS: 117 19:02:06 -484.430236 0.204077
LBFGS: 118 19:02:06 -484.452477 0.252451
LBFGS: 119 19:02:07 -484.475909 0.273568
LBFGS: 120 19:02:07 -484.498683 0.301674
LBFGS: 121 19:02:08 -484.518715 0.308904
LBFGS: 122 19:02:08 -484.537707 0.230892
LBFGS: 123 19:02:09 -484.559027 0.203116
LBFGS: 124 19:02:09 -484.580842 0.256442
LBFGS: 125 19:02:10 -484.603562 0.279154
LBFGS: 126 19:02:10 -484.623792 0.214331
LBFGS: 127 19:02:11 -484.642449 0.210542
LBFGS: 128 19:02:11 -484.661975 0.295669
LBFGS: 129 19:02:11 -484.689154 0.401151
LBFGS: 130 19:02:12 -484.718332 0.308726
LBFGS: 131 19:02:12 -484.741818 0.382969
LBFGS: 132 19:02:13 -484.763953 0.216638
LBFGS: 133 19:02:13 -484.787856 0.235513
LBFGS: 134 19:02:14 -484.812531 0.264937
LBFGS: 135 19:02:14 -484.835766 0.402124
LBFGS: 136 19:02:15 -484.858430 0.217953
LBFGS: 137 19:02:15 -484.877321 0.179554
LBFGS: 138 19:02:16 -484.898387 0.261446
LBFGS: 139 19:02:16 -484.921435 0.243394
LBFGS: 140 19:02:17 -484.948703 0.319621
LBFGS: 141 19:02:17 -484.971011 0.261375
LBFGS: 142 19:02:17 -484.991352 0.230271
LBFGS: 143 19:02:18 -485.011476 0.211258
LBFGS: 144 19:02:18 -485.036650 0.291015
LBFGS: 145 19:02:19 -485.059316 0.183163
LBFGS: 146 19:02:19 -485.079177 0.199940
LBFGS: 147 19:02:20 -485.097575 0.197279
LBFGS: 148 19:02:20 -485.115220 0.225396
LBFGS: 149 19:02:21 -485.131850 0.206028
LBFGS: 150 19:02:21 -485.148505 0.180702
LBFGS: 151 19:02:22 -485.164133 0.192611
LBFGS: 152 19:02:22 -485.179739 0.192113
LBFGS: 153 19:02:23 -485.193961 0.157355
LBFGS: 154 19:02:23 -485.206883 0.150161
LBFGS: 155 19:02:24 -485.217582 0.131592
LBFGS: 156 19:02:24 -485.226837 0.132444
LBFGS: 157 19:02:24 -485.236188 0.135832
LBFGS: 158 19:02:25 -485.246934 0.128134
LBFGS: 159 19:02:25 -485.258847 0.150498
LBFGS: 160 19:02:26 -485.271095 0.170130
LBFGS: 161 19:02:26 -485.282843 0.206553
LBFGS: 162 19:02:27 -485.293838 0.155075
LBFGS: 163 19:02:27 -485.304935 0.155148
LBFGS: 164 19:02:28 -485.316105 0.131736
LBFGS: 165 19:02:28 -485.327063 0.189752
LBFGS: 166 19:02:29 -485.337150 0.153041
LBFGS: 167 19:02:29 -485.347754 0.150834
LBFGS: 168 19:02:30 -485.359310 0.153122
LBFGS: 169 19:02:30 -485.371676 0.162032
LBFGS: 170 19:02:31 -485.382159 0.141829
LBFGS: 171 19:02:31 -485.390717 0.119533
LBFGS: 172 19:02:31 -485.399287 0.143391
LBFGS: 173 19:02:32 -485.410824 0.179853
LBFGS: 174 19:02:32 -485.424947 0.205613
LBFGS: 175 19:02:33 -485.438451 0.241444
LBFGS: 176 19:02:33 -485.448004 0.214438
LBFGS: 177 19:02:34 -485.456397 0.134944
LBFGS: 178 19:02:34 -485.464157 0.134600
LBFGS: 179 19:02:35 -485.473787 0.186862
LBFGS: 180 19:02:35 -485.480682 0.173867
LBFGS: 181 19:02:36 -485.487156 0.115708
LBFGS: 182 19:02:36 -485.493831 0.128686
LBFGS: 183 19:02:37 -485.501392 0.116803
LBFGS: 184 19:02:37 -485.508188 0.154473
LBFGS: 185 19:02:38 -485.513987 0.102476
LBFGS: 186 19:02:38 -485.519603 0.105021
LBFGS: 187 19:02:39 -485.525997 0.152851
LBFGS: 188 19:02:39 -485.532837 0.173253
LBFGS: 189 19:02:39 -485.538829 0.115083
LBFGS: 190 19:02:40 -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