From 2687e66608ffcae73db598865097543f6810343a Mon Sep 17 00:00:00 2001 From: Niklas Kappel Date: Thu, 25 Apr 2024 14:34:41 +0200 Subject: [PATCH] Strip trailing new lines and update example for realsitic pressure --- README.md | 8 +- examples/create_o2_box.py | 4 +- examples/o2_box.lmpdat | 402 ++++++++++++++++++++++++++++++++++++-- examples/o2_box.mol | 394 +++++++++++++++++++++++++++++++++++-- pyproject.toml | 2 +- src/molbox/lammps_data.py | 2 + 6 files changed, 768 insertions(+), 44 deletions(-) diff --git a/README.md b/README.md index 1338476..ec61562 100644 --- a/README.md +++ b/README.md @@ -14,18 +14,20 @@ pip install molbox from molbox import Box, MolBox from molbox.lammps_data import write_lammps_data from molbox.rdkit_3d_ops import create_3d_mol_from_smiles, rotate_mol +from rdkit import Chem from scipy.spatial.transform import Rotation def main(): - box = Box([0, 0, 0], [10, 10, 10]) + box = Box([0, 0, 0], [175, 175, 175]) o2_box = MolBox(box=box) o2_mol = create_3d_mol_from_smiles("O=O") - num_mols = 32 + num_mols = 128 for _ in range(num_mols): - rotation = Rotation.random(random_state=42) + rotation = Rotation.random() new_mol = rotate_mol(o2_mol, rotation, "COM") o2_box.add_mol_randomly(new_mol) + Chem.MolToMolFile(o2_box.mol, "examples/o2_box.mol") write_lammps_data(o2_box, "examples/o2_box.lmpdat") diff --git a/examples/create_o2_box.py b/examples/create_o2_box.py index 7e2414e..2309d2f 100644 --- a/examples/create_o2_box.py +++ b/examples/create_o2_box.py @@ -6,10 +6,10 @@ def main(): - box = Box([0, 0, 0], [10, 10, 10]) + box = Box([0, 0, 0], [175, 175, 175]) o2_box = MolBox(box=box) o2_mol = create_3d_mol_from_smiles("O=O") - num_mols = 8 + num_mols = 128 for _ in range(num_mols): rotation = Rotation.random() new_mol = rotate_mol(o2_mol, rotation, "COM") diff --git a/examples/o2_box.lmpdat b/examples/o2_box.lmpdat index be42cc1..2f3ea06 100644 --- a/examples/o2_box.lmpdat +++ b/examples/o2_box.lmpdat @@ -1,6 +1,6 @@ LAMMPS data file generated by OpenBabel -16 atoms -8 bonds +256 atoms +128 bonds 0 angles 0 dihedrals 0 impropers @@ -9,9 +9,9 @@ LAMMPS data file generated by OpenBabel 0 angle types 0 dihedral types 0 improper types - 0.00000 10.00000 xlo xhi - 0.00000 10.00000 ylo yhi - 0.00000 10.00000 zlo zhi + 0.00000 175.00000 xlo xhi + 0.00000 175.00000 ylo yhi + 0.00000 175.00000 zlo zhi @@ -22,22 +22,262 @@ Masses Atoms -1 1 1 -0.82000 3.04790 5.53610 0.71000 # O -2 1 1 -0.82000 2.14000 5.73890 0.03630 # O -3 2 1 -0.82000 2.10050 6.36320 8.52250 # O -4 2 1 -0.82000 2.10820 5.83190 9.54070 # O -5 3 1 -0.82000 8.42040 2.22030 6.26960 # O -6 3 1 -0.82000 8.66790 3.15150 5.64440 # O -7 4 1 -0.82000 8.22650 6.89940 7.71260 # O -8 4 1 -0.82000 9.19870 7.46980 7.49220 # O -9 5 1 -0.82000 3.37570 0.09190 2.45610 # O -10 5 1 -0.82000 4.08420 0.82470 1.92680 # O -11 6 1 -0.82000 7.50930 9.85370 0.45760 # O -12 6 1 -0.82000 7.40900 9.78110 1.59950 # O -13 7 1 -0.82000 9.31140 2.93000 4.46270 # O -14 7 1 -0.82000 8.69150 3.63750 5.12180 # O -15 8 1 -0.82000 9.99520 8.43210 0.05480 # O -16 8 1 -0.82000 8.88860 8.43980 0.36240 # O +1 1 1 -0.82000 141.86320 152.56810 58.46760 # O +2 1 1 -0.82000 141.11750 151.70810 58.31410 # O +3 2 1 -0.82000 134.93600 13.42930 153.55740 # O +4 2 1 -0.82000 135.83080 13.60090 154.25680 # O +5 3 1 -0.82000 66.82000 158.22610 116.08740 # O +6 3 1 -0.82000 65.93920 157.52110 116.30280 # O +7 4 1 -0.82000 144.56610 33.09100 134.02180 # O +8 4 1 -0.82000 145.44010 32.88160 133.30670 # O +9 5 1 -0.82000 167.94770 159.30290 64.39480 # O +10 5 1 -0.82000 167.06180 158.59900 64.19720 # O +11 6 1 -0.82000 19.73170 4.74270 66.02980 # O +12 6 1 -0.82000 19.33560 3.80700 66.56540 # O +13 7 1 -0.82000 114.14580 151.74740 69.66470 # O +14 7 1 -0.82000 114.32430 152.35130 70.62530 # O +15 8 1 -0.82000 135.59540 161.75800 70.90830 # O +16 8 1 -0.82000 134.66100 162.24070 71.36980 # O +17 9 1 -0.82000 133.91130 132.31570 56.17600 # O +18 9 1 -0.82000 132.91220 132.85850 56.01390 # O +19 10 1 -0.82000 47.70560 25.11320 115.32310 # O +20 10 1 -0.82000 46.62240 25.29820 114.98890 # O +21 11 1 -0.82000 110.61200 76.32610 166.64490 # O +22 11 1 -0.82000 109.69150 75.65630 166.79700 # O +23 12 1 -0.82000 69.77050 23.92030 117.96910 # O +24 12 1 -0.82000 69.84130 22.77410 117.98680 # O +25 13 1 -0.82000 24.81090 100.00900 140.03930 # O +26 13 1 -0.82000 25.14980 98.97140 139.68200 # O +27 14 1 -0.82000 143.53400 81.60200 152.06830 # O +28 14 1 -0.82000 143.60900 82.19800 153.04730 # O +29 15 1 -0.82000 39.94150 116.40050 47.02040 # O +30 15 1 -0.82000 39.51200 115.50910 47.60360 # O +31 16 1 -0.82000 104.69600 139.37910 90.35990 # O +32 16 1 -0.82000 104.74130 138.24650 90.54500 # O +33 17 1 -0.82000 6.94030 156.00650 168.26520 # O +34 17 1 -0.82000 6.78200 155.36740 167.32410 # O +35 18 1 -0.82000 120.63020 3.79460 118.93930 # O +36 18 1 -0.82000 120.03490 4.77680 118.93390 # O +37 19 1 -0.82000 5.88480 25.54650 168.01080 # O +38 19 1 -0.82000 5.64620 25.32870 166.90860 # O +39 20 1 -0.82000 163.83480 54.94010 33.34050 # O +40 20 1 -0.82000 163.28630 55.86060 33.75420 # O +41 21 1 -0.82000 118.18520 6.09500 95.87000 # O +42 21 1 -0.82000 118.18940 6.19100 94.72550 # O +43 22 1 -0.82000 5.47390 165.89460 24.51620 # O +44 22 1 -0.82000 6.15120 166.82090 24.46590 # O +45 23 1 -0.82000 153.73110 141.66870 79.01900 # O +46 23 1 -0.82000 152.75510 142.07990 78.57480 # O +47 24 1 -0.82000 120.48030 125.16770 117.87780 # O +48 24 1 -0.82000 121.60400 124.95750 117.76730 # O +49 25 1 -0.82000 115.13560 77.93920 43.26550 # O +50 25 1 -0.82000 114.39670 78.01290 44.14180 # O +51 26 1 -0.82000 31.56880 29.42530 21.80650 # O +52 26 1 -0.82000 31.68040 28.48780 22.46060 # O +53 27 1 -0.82000 53.83630 134.04620 14.69810 # O +54 27 1 -0.82000 54.19230 133.87410 15.77640 # O +55 28 1 -0.82000 49.02070 137.63690 20.18830 # O +56 28 1 -0.82000 49.98650 137.84480 19.60260 # O +57 29 1 -0.82000 97.20570 134.21020 126.97790 # O +58 29 1 -0.82000 98.34880 134.26900 127.07230 # O +59 30 1 -0.82000 172.70710 163.85800 6.91430 # O +60 30 1 -0.82000 173.33840 163.99540 7.86390 # O +61 31 1 -0.82000 14.07660 55.84560 53.76880 # O +62 31 1 -0.82000 14.54410 56.11710 54.78210 # O +63 32 1 -0.82000 65.27780 86.31330 134.71460 # O +64 32 1 -0.82000 65.54700 85.19670 134.71800 # O +65 33 1 -0.82000 101.59680 128.48670 106.06440 # O +66 33 1 -0.82000 101.49670 127.41600 106.46770 # O +67 34 1 -0.82000 119.45760 117.87840 141.78160 # O +68 34 1 -0.82000 119.85970 117.29130 140.88000 # O +69 35 1 -0.82000 80.17830 171.89720 61.04120 # O +70 35 1 -0.82000 79.69220 170.85690 61.01620 # O +71 36 1 -0.82000 39.40400 37.54860 42.02020 # O +72 36 1 -0.82000 39.72760 36.87600 41.14720 # O +73 37 1 -0.82000 84.76470 70.80270 105.54950 # O +74 37 1 -0.82000 84.37560 71.02330 104.49160 # O +75 38 1 -0.82000 93.76620 115.15210 161.04160 # O +76 38 1 -0.82000 93.27650 116.03130 160.48800 # O +77 39 1 -0.82000 73.30140 85.37440 2.35150 # O +78 39 1 -0.82000 74.02230 86.02630 1.73950 # O +79 40 1 -0.82000 56.83690 2.06470 33.00250 # O +80 40 1 -0.82000 55.94760 1.33950 32.95260 # O +81 41 1 -0.82000 52.85480 26.10720 127.96450 # O +82 41 1 -0.82000 53.49620 26.03660 127.01430 # O +83 42 1 -0.82000 88.22060 120.73500 150.78220 # O +84 42 1 -0.82000 88.39850 121.85260 150.97840 # O +85 43 1 -0.82000 91.04360 121.20090 46.60940 # O +86 43 1 -0.82000 90.76050 120.69320 47.60010 # O +87 44 1 -0.82000 116.74740 87.53460 89.83220 # O +88 44 1 -0.82000 117.63220 86.98900 89.34370 # O +89 45 1 -0.82000 18.60150 164.30620 152.03030 # O +90 45 1 -0.82000 17.53690 164.72990 151.95050 # O +91 46 1 -0.82000 17.47620 58.89730 62.99140 # O +92 46 1 -0.82000 18.56020 58.63550 62.71640 # O +93 47 1 -0.82000 85.32740 26.05480 33.73040 # O +94 47 1 -0.82000 85.81480 25.48950 34.60340 # O +95 48 1 -0.82000 11.69780 70.07840 166.65190 # O +96 48 1 -0.82000 12.49750 69.25690 166.72210 # O +97 49 1 -0.82000 70.48530 60.39760 24.78040 # O +98 49 1 -0.82000 70.37610 59.25780 24.69100 # O +99 50 1 -0.82000 57.14580 113.84210 100.73580 # O +100 50 1 -0.82000 56.57260 113.72260 101.72380 # O +101 51 1 -0.82000 82.09940 3.21970 37.43300 # O +102 51 1 -0.82000 83.02390 3.39460 36.77430 # O +103 52 1 -0.82000 159.58830 107.66750 31.18270 # O +104 52 1 -0.82000 158.85430 107.04720 31.81180 # O +105 53 1 -0.82000 27.84720 70.11610 49.94250 # O +106 53 1 -0.82000 28.38660 69.35320 50.61050 # O +107 54 1 -0.82000 122.04080 5.07300 0.93650 # O +108 54 1 -0.82000 121.07250 5.62620 0.66170 # O +109 55 1 -0.82000 118.19620 102.05900 20.05620 # O +110 55 1 -0.82000 119.12830 101.87180 20.70060 # O +111 56 1 -0.82000 68.86390 124.29620 111.88190 # O +112 56 1 -0.82000 69.64670 124.12350 112.70430 # O +113 57 1 -0.82000 154.50370 75.83170 113.90130 # O +114 57 1 -0.82000 154.55450 76.46940 112.94740 # O +115 58 1 -0.82000 28.42350 78.53820 162.03320 # O +116 58 1 -0.82000 27.56840 79.12060 161.53420 # O +117 59 1 -0.82000 69.92650 117.43850 45.58670 # O +118 59 1 -0.82000 70.69420 117.47660 46.44010 # O +119 60 1 -0.82000 0.56570 132.34060 127.59080 # O +120 60 1 -0.82000 1.42000 132.85360 127.01980 # O +121 61 1 -0.82000 28.74600 166.46760 86.16190 # O +122 61 1 -0.82000 28.54080 165.36640 85.90830 # O +123 62 1 -0.82000 90.71740 67.42260 126.41690 # O +124 62 1 -0.82000 89.65620 67.74800 126.71230 # O +125 63 1 -0.82000 24.04550 18.45420 72.19220 # O +126 63 1 -0.82000 24.65900 19.00850 72.98950 # O +127 64 1 -0.82000 79.70590 80.31620 86.18820 # O +128 64 1 -0.82000 80.13140 81.04770 86.96480 # O +129 65 1 -0.82000 15.08330 76.18980 112.74610 # O +130 65 1 -0.82000 14.00940 75.83440 112.94500 # O +131 66 1 -0.82000 75.38210 171.25330 10.08200 # O +132 66 1 -0.82000 76.13150 170.39900 10.24810 # O +133 67 1 -0.82000 72.32490 168.96140 139.13500 # O +134 67 1 -0.82000 72.95540 168.74410 140.07010 # O +135 68 1 -0.82000 117.78610 21.00990 155.48850 # O +136 68 1 -0.82000 117.75970 20.09260 154.79780 # O +137 69 1 -0.82000 42.76180 121.18330 37.63770 # O +138 69 1 -0.82000 42.26910 122.22070 37.65180 # O +139 70 1 -0.82000 129.98090 117.34440 93.76370 # O +140 70 1 -0.82000 129.65310 118.39930 94.07820 # O +141 71 1 -0.82000 112.73580 113.45610 1.76110 # O +142 71 1 -0.82000 112.58580 114.57070 1.52790 # O +143 72 1 -0.82000 37.64430 16.06490 1.24390 # O +144 72 1 -0.82000 37.80390 15.16540 1.93990 # O +145 73 1 -0.82000 98.27390 68.39620 14.27520 # O +146 73 1 -0.82000 99.36070 68.45300 14.64250 # O +147 74 1 -0.82000 78.44520 173.19390 120.65930 # O +148 74 1 -0.82000 78.09250 172.10100 120.63660 # O +149 75 1 -0.82000 11.54630 25.47130 68.70890 # O +150 75 1 -0.82000 11.51120 25.95980 67.67000 # O +151 76 1 -0.82000 100.54860 46.49420 68.18800 # O +152 76 1 -0.82000 100.58420 45.94360 67.18070 # O +153 77 1 -0.82000 32.28660 150.65830 92.98510 # O +154 77 1 -0.82000 32.75740 151.29410 93.81780 # O +155 78 1 -0.82000 142.76560 64.27220 10.08900 # O +156 78 1 -0.82000 143.37800 63.50780 10.68890 # O +157 79 1 -0.82000 86.97690 32.16710 37.09320 # O +158 79 1 -0.82000 86.54120 31.24270 36.56890 # O +159 80 1 -0.82000 137.47260 20.85060 115.97370 # O +160 80 1 -0.82000 136.45220 20.35920 115.78280 # O +161 81 1 -0.82000 157.72710 0.52740 138.06590 # O +162 81 1 -0.82000 157.06740 0.50200 137.12600 # O +163 82 1 -0.82000 84.90680 36.48290 150.50820 # O +164 82 1 -0.82000 85.47470 37.34830 150.01050 # O +165 83 1 -0.82000 45.89590 62.28650 140.70980 # O +166 83 1 -0.82000 46.88460 61.72200 140.86100 # O +167 84 1 -0.82000 2.83910 142.31960 151.92090 # O +168 84 1 -0.82000 3.85380 142.23220 151.38990 # O +169 85 1 -0.82000 162.95560 126.55780 87.29900 # O +170 85 1 -0.82000 164.00150 126.59960 87.77180 # O +171 86 1 -0.82000 0.79160 3.50160 42.80500 # O +172 86 1 -0.82000 1.14760 2.59950 43.42040 # O +173 87 1 -0.82000 2.51610 164.98190 114.75570 # O +174 87 1 -0.82000 2.85420 166.02450 114.41260 # O +175 88 1 -0.82000 84.24190 84.95990 143.90120 # O +176 88 1 -0.82000 85.35160 84.70670 143.74770 # O +177 89 1 -0.82000 95.19450 157.12610 16.40050 # O +178 89 1 -0.82000 95.49410 157.37330 15.31960 # O +179 90 1 -0.82000 3.80770 79.76200 41.20450 # O +180 90 1 -0.82000 4.85430 79.76210 40.73140 # O +181 91 1 -0.82000 170.58140 65.90910 134.74880 # O +182 91 1 -0.82000 171.46350 65.19010 134.59380 # O +183 92 1 -0.82000 172.00300 0.19890 3.22350 # O +184 92 1 -0.82000 172.28540 0.48480 2.14760 # O +185 93 1 -0.82000 76.83660 5.68590 144.79640 # O +186 93 1 -0.82000 76.23450 5.47530 143.84130 # O +187 94 1 -0.82000 120.81100 137.12830 103.37640 # O +188 94 1 -0.82000 120.95830 137.91770 102.55530 # O +189 95 1 -0.82000 111.94290 43.95770 138.64560 # O +190 95 1 -0.82000 112.84030 44.53590 138.22170 # O +191 96 1 -0.82000 75.09880 74.91850 128.49000 # O +192 96 1 -0.82000 75.64590 75.92720 128.54060 # O +193 97 1 -0.82000 149.09720 20.95090 90.92930 # O +194 97 1 -0.82000 148.46330 21.24840 90.01890 # O +195 98 1 -0.82000 26.93370 62.80920 154.11260 # O +196 98 1 -0.82000 27.50390 62.86500 155.10810 # O +197 99 1 -0.82000 104.10800 170.69730 146.64120 # O +198 99 1 -0.82000 105.16500 170.24780 146.63200 # O +199 100 1 -0.82000 27.79330 107.86920 151.90140 # O +200 100 1 -0.82000 28.08740 106.80080 152.20340 # O +201 101 1 -0.82000 97.32050 107.01720 14.20420 # O +202 101 1 -0.82000 98.07020 106.85360 15.05880 # O +203 102 1 -0.82000 152.33300 141.09120 63.48950 # O +204 102 1 -0.82000 152.76640 140.72880 64.48960 # O +205 103 1 -0.82000 47.68160 92.52340 105.90640 # O +206 103 1 -0.82000 47.87760 91.39510 105.81940 # O +207 104 1 -0.82000 108.42700 125.07090 23.28840 # O +208 104 1 -0.82000 108.83450 124.08900 23.72320 # O +209 105 1 -0.82000 24.52610 129.48650 35.26860 # O +210 105 1 -0.82000 24.21000 128.61970 34.58460 # O +211 106 1 -0.82000 19.70220 100.43510 98.52010 # O +212 106 1 -0.82000 18.94240 99.97710 97.79060 # O +213 107 1 -0.82000 152.92070 130.23650 93.09380 # O +214 107 1 -0.82000 153.14100 130.82950 94.05240 # O +215 108 1 -0.82000 111.98540 74.58180 31.98280 # O +216 108 1 -0.82000 112.02250 73.49680 32.35750 # O +217 109 1 -0.82000 31.96890 102.48700 121.83320 # O +218 109 1 -0.82000 31.08110 101.79350 121.60930 # O +219 110 1 -0.82000 120.26500 151.79180 48.55360 # O +220 110 1 -0.82000 120.71380 150.76660 48.81210 # O +221 111 1 -0.82000 118.83340 66.87290 45.99230 # O +222 111 1 -0.82000 119.78540 66.57960 46.56410 # O +223 112 1 -0.82000 97.66050 50.16650 115.40050 # O +224 112 1 -0.82000 96.98490 50.67130 114.62090 # O +225 113 1 -0.82000 127.59550 116.84880 116.39340 # O +226 113 1 -0.82000 126.58790 116.77560 116.93970 # O +227 114 1 -0.82000 116.03490 48.02740 11.22030 # O +228 114 1 -0.82000 116.20010 48.63600 12.18020 # O +229 115 1 -0.82000 152.88360 147.37540 113.09650 # O +230 115 1 -0.82000 152.03970 147.44540 113.87240 # O +231 116 1 -0.82000 80.17090 96.73580 57.65550 # O +232 116 1 -0.82000 80.30060 96.12150 58.61730 # O +233 117 1 -0.82000 137.76220 97.08310 139.76450 # O +234 117 1 -0.82000 137.06130 97.96580 139.54320 # O +235 118 1 -0.82000 80.40810 56.23960 12.66780 # O +236 118 1 -0.82000 81.31660 56.06110 13.34750 # O +237 119 1 -0.82000 38.30410 159.13370 97.44950 # O +238 119 1 -0.82000 37.56860 159.30940 96.58500 # O +239 120 1 -0.82000 75.10220 129.78950 87.41490 # O +240 120 1 -0.82000 74.45690 128.84000 87.44810 # O +241 121 1 -0.82000 20.21170 152.24420 40.15020 # O +242 121 1 -0.82000 19.37940 152.72450 40.77920 # O +243 122 1 -0.82000 33.74300 106.55210 41.16270 # O +244 122 1 -0.82000 34.42770 107.41840 41.47870 # O +245 123 1 -0.82000 85.43420 35.28890 7.57950 # O +246 123 1 -0.82000 85.62440 35.03090 8.68240 # O +247 124 1 -0.82000 155.02820 126.80690 170.48480 # O +248 124 1 -0.82000 154.43250 125.82890 170.57320 # O +249 125 1 -0.82000 25.87160 172.04290 135.58990 # O +250 125 1 -0.82000 25.87560 172.30490 136.70820 # O +251 126 1 -0.82000 84.64150 173.29710 99.08650 # O +252 126 1 -0.82000 85.62030 173.88670 99.20280 # O +253 127 1 -0.82000 100.31470 45.88510 18.53330 # O +254 127 1 -0.82000 101.08540 45.13150 18.13690 # O +255 128 1 -0.82000 80.81310 110.20860 142.47220 # O +256 128 1 -0.82000 80.90890 109.13000 142.08940 # O Bonds @@ -50,6 +290,126 @@ Bonds 6 1 11 12 # O: O 7 1 13 14 # O: O 8 1 15 16 # O: O +9 1 17 18 # O: O +10 1 19 20 # O: O +11 1 21 22 # O: O +12 1 23 24 # O: O +13 1 25 26 # O: O +14 1 27 28 # O: O +15 1 29 30 # O: O +16 1 31 32 # O: O +17 1 33 34 # O: O +18 1 35 36 # O: O +19 1 37 38 # O: O +20 1 39 40 # O: O +21 1 41 42 # O: O +22 1 43 44 # O: O +23 1 45 46 # O: O +24 1 47 48 # O: O +25 1 49 50 # O: O +26 1 51 52 # O: O +27 1 53 54 # O: O +28 1 55 56 # O: O +29 1 57 58 # O: O +30 1 59 60 # O: O +31 1 61 62 # O: O +32 1 63 64 # O: O +33 1 65 66 # O: O +34 1 67 68 # O: O +35 1 69 70 # O: O +36 1 71 72 # O: O +37 1 73 74 # O: O +38 1 75 76 # O: O +39 1 77 78 # O: O +40 1 79 80 # O: O +41 1 81 82 # O: O +42 1 83 84 # O: O +43 1 85 86 # O: O +44 1 87 88 # O: O +45 1 89 90 # O: O +46 1 91 92 # O: O +47 1 93 94 # O: O +48 1 95 96 # O: O +49 1 97 98 # O: O +50 1 99 100 # O: O +51 1 101 102 # O: O +52 1 103 104 # O: O +53 1 105 106 # O: O +54 1 107 108 # O: O +55 1 109 110 # O: O +56 1 111 112 # O: O +57 1 113 114 # O: O +58 1 115 116 # O: O +59 1 117 118 # O: O +60 1 119 120 # O: O +61 1 121 122 # O: O +62 1 123 124 # O: O +63 1 125 126 # O: O +64 1 127 128 # O: O +65 1 129 130 # O: O +66 1 131 132 # O: O +67 1 133 134 # O: O +68 1 135 136 # O: O +69 1 137 138 # O: O +70 1 139 140 # O: O +71 1 141 142 # O: O +72 1 143 144 # O: O +73 1 145 146 # O: O +74 1 147 148 # O: O +75 1 149 150 # O: O +76 1 151 152 # O: O +77 1 153 154 # O: O +78 1 155 156 # O: O +79 1 157 158 # O: O +80 1 159 160 # O: O +81 1 161 162 # O: O +82 1 163 164 # O: O +83 1 165 166 # O: O +84 1 167 168 # O: O +85 1 169 170 # O: O +86 1 171 172 # O: O +87 1 173 174 # O: O +88 1 175 176 # O: O +89 1 177 178 # O: O +90 1 179 180 # O: O +91 1 181 182 # O: O +92 1 183 184 # O: O +93 1 185 186 # O: O +94 1 187 188 # O: O +95 1 189 190 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b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "molbox" -version = "0.1.2" +version = "0.1.3" description = "Create simulation boxes for LAMMPS." authors = ["Niklas Kappel "] readme = "README.md" diff --git a/src/molbox/lammps_data.py b/src/molbox/lammps_data.py index 0bdb5ae..a5d10a5 100644 --- a/src/molbox/lammps_data.py +++ b/src/molbox/lammps_data.py @@ -25,5 +25,7 @@ def write_lammps_data(molbox: MolBox, filename: str) -> None: pattern = r".*xlo xhi\n.*ylo yhi\n.*zlo zhi" lmpdata_block = re.sub(pattern, box_section, lmpdata_block) + lmpdata_block = lmpdata_block.rstrip() + "\n" + with open(filename, "w") as f: f.write(lmpdata_block)