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StephMcCallumStephMcCallum
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remove files, merge
2 parents 8c3336f + 0035b1f commit 5fa9efd

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5 files changed

+380
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‎P3HT.mol2

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@<TRIPOS>MOLECULE
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RES
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27 27 1 0 1
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SMALL
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NO_CHARGES
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@<TRIPOS>CRYSIN
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13.8222 9.4717 9.3109 90.0000 90.0000 90.0000 1 1
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@<TRIPOS>ATOM
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1 C0 14.1713 10.6638 10.2575 C0 1 RES
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2 C0 12.7816 10.5396 9.6397 C0 1 RES
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3 C0 11.8555 9.6942 10.5225 C0 1 RES
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4 C0 10.4652 9.5693 9.8894 C0 1 RES
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5 C0 9.5345 8.7093 10.7585 C0 1 RES
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6 C0 8.1488 8.5349 10.1180 C0 1 RES
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7 C1 7.4178 9.8420 9.9706 C1 1 RES
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8 C1 7.0527 10.6406 11.0504 C1 1 RES
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9 S2 6.2624 11.9995 10.4564 S2 1 RES
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10 C1 6.3741 11.5898 8.8302 C1 1 RES
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11 C1 7.0354 10.3740 8.7296 C1 1 RES
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12 H3 14.8183 11.2776 9.5959 H3 1 RES
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13 H3 14.6325 9.6595 10.3735 H3 1 RES
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14 H3 14.1093 11.1550 11.2515 H3 1 RES
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15 H3 12.8767 10.0661 8.6379 H3 1 RES
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16 H3 12.3520 11.5574 9.5139 H3 1 RES
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17 H3 12.2944 8.6797 10.6472 H3 1 RES
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18 H3 11.7630 10.1704 11.5235 H3 1 RES
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19 H3 10.0306 10.5856 9.7667 H3 1 RES
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20 H3 10.5621 9.0987 8.8861 H3 1 RES
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21 H3 9.9875 7.7008 10.8798 H3 1 RES
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22 H3 9.4290 9.1641 11.7676 H3 1 RES
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23 H3 7.5352 7.8577 10.7499 H3 1 RES
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24 H3 8.2742 8.0520 9.1238 H3 1 RES
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25 H4 7.2362 9.8904 7.7826 H4 1 RES
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26 H5 7.2416 10.4260 12.0935 H5 1 RES
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27 H5 5.9961 12.1726 8.0013 H5 1 RES
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@<TRIPOS>BOND
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1 1 2 1
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2 1 12 1
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3 1 13 1
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4 1 14 1
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5 2 3 1
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6 2 15 1
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7 2 16 1
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8 3 4 1
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9 3 17 1
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10 3 18 1
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11 4 5 1
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12 4 19 1
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13 4 20 1
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14 5 6 1
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15 5 21 1
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16 5 22 1
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17 6 7 1
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18 6 23 1
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19 6 24 1
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20 7 8 1
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21 7 11 1
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22 8 9 1
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23 8 26 1
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24 9 10 1
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25 10 11 1
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26 10 27 1
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27 11 25 1
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@<TRIPOS>SUBSTRUCTURE
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1 RES 1 RESIDUE 0 **** ROOT 0

‎P3HT.xml

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<ForceField name="" version="" combining_rule="geometric">
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<AtomTypes>
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<Type name="H5" class="H5" element="_H5" mass="1.008" def="_H5" desc=""/>
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<Type name="H3" class="H3" element="_H3" mass="1.008" def="_H3" desc=""/>
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<Type name="H4" class="H4" element="_H4" mass="1.008" def="_H4" desc=""/>
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<Type name="S2" class="S2" element="_S2" mass="32.06" def="_S2" desc=""/>
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<Type name="C0" class="C0" element="_C0" mass="12.011" def="_C0" desc=""/>
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<Type name="C1" class="C1" element="_C1" mass="12.011" def="_C1" desc=""/>
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</AtomTypes>
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<HarmonicBondForce>
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<Bond class1="C0" class2="C0" length="0.15393138859485156" k="216071.5673604569"/>
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<Bond class1="C0" class2="H3" length="0.10976204613301968" k="306243.2994478932"/>
13+
<Bond class1="C0" class2="C1" length="0.15021762614242648" k="245043.09124482484"/>
14+
<Bond class1="C1" class2="C1" length="0.13696133519685275" k="417404.23786464764"/>
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<Bond class1="C1" class2="S2" length="0.17644359746123384" k="146619.58148765477"/>
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<Bond class1="C1" class2="H5" length="0.10847683421363911" k="342520.45189188817"/>
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<Bond class1="S2" class2="C1" length="0.17456724887079533" k="155523.3472930218"/>
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<Bond class1="C1" class2="H4" length="0.10863386001736958" k="335143.64070747164"/>
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</HarmonicBondForce>
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<HarmonicAngleForce>
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<Angle class1="C0" class2="C0" class3="C0" angle="1.971023440361023" k="571.7145128119677"/>
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<Angle class1="C0" class2="C0" class3="H3" angle="1.919396162033081" k="400.7807950494681"/>
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<Angle class1="C0" class2="C0" class3="C1" angle="1.9725769758224487" k="567.2166987593794"/>
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<Angle class1="C0" class2="C1" class3="C1" angle="2.387712240219116" k="370.1760901705978"/>
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<Angle class1="C1" class2="C0" class3="H3" angle="1.916161298751831" k="419.6637425240785"/>
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<Angle class1="C1" class2="C1" class3="S2" angle="2.26436710357666" k="600.522063868667"/>
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<Angle class1="C1" class2="C1" class3="H5" angle="2.385676145553589" k="242.64219357507048"/>
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<Angle class1="C1" class2="C1" class3="C1" angle="2.221386194229126" k="622.0677222701529"/>
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<Angle class1="C1" class2="C1" class3="H4" angle="2.2988548278808594" k="253.7424039841016"/>
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<Angle class1="C1" class2="S2" class3="C1" angle="1.749892234802246" k="1116.8353273914954"/>
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<Angle class1="S2" class2="C1" class3="H5" angle="2.220374345779419" k="269.41800934151877"/>
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<Angle class1="S2" class2="C1" class3="C1" angle="2.220290422439575" k="647.3334296165826"/>
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<Angle class1="H3" class2="C0" class3="H3" angle="1.889668583869934" k="334.4416957736681"/>
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</HarmonicAngleForce>
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<PeriodicTorsionForce>
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<Proper class1="C0" class2="C0" class3="C0" class4="C0" periodicity1="1" k1="0.4446541383098747" phase1="3.141592653589793" periodicity2="2" k2="1.0641324288535725" phase2="3.141592653589793" periodicity3="3" k3="0.6187414486983862" phase3="0.0" periodicity4="4" k4="0.5066066972730099" phase4="3.141592653589793"/>
37+
<Proper class1="C0" class2="C0" class3="C0" class4="H3" periodicity1="1" k1="0.5465327435421055" phase1="3.141592653589793" periodicity2="2" k2="0.7277209918403849" phase2="3.141592653589793" periodicity3="3" k3="0.6779125309414975" phase3="0.0" periodicity4="4" k4="0.5867722704365655" phase4="3.141592653589793"/>
38+
<Proper class1="C0" class2="C0" class3="C0" class4="C1" periodicity1="1" k1="0.5332706983018924" phase1="3.141592653589793" periodicity2="2" k2="0.6781320628943731" phase2="3.141592653589793" periodicity3="3" k3="0.6463249164829086" phase3="0.0" periodicity4="4" k4="0.4977203525254705" phase4="3.141592653589793"/>
39+
<Proper class1="C0" class2="C0" class3="C1" class4="C1" periodicity1="1" k1="0.12238527177792649" phase1="3.141592653589793" periodicity2="2" k2="0.7807330298796531" phase2="3.141592653589793" periodicity3="3" k3="0.1774644193997523" phase3="0.0" periodicity4="4" k4="0.09216524281414898" phase4="3.141592653589793"/>
40+
<Proper class1="C0" class2="C1" class3="C1" class4="S2" periodicity1="1" k1="0.5786208954379767" phase1="3.141592653589793" periodicity2="2" k2="2.842784895778366" phase2="3.141592653589793" periodicity3="3" k3="0.7710115009187717" phase3="0.0" periodicity4="4" k4="1.1263615231934767" phase4="3.141592653589793"/>
41+
<Proper class1="C0" class2="C1" class3="C1" class4="H5" periodicity1="1" k1="0.7395275776749591" phase1="3.141592653589793" periodicity2="2" k2="2.7895061031106647" phase2="3.141592653589793" periodicity3="3" k3="1.0461584698966508" phase3="0.0" periodicity4="4" k4="1.0942429210772013" phase4="3.141592653589793"/>
42+
<Proper class1="C0" class2="C1" class3="C1" class4="C1" periodicity1="1" k1="0.538864636847019" phase1="3.141592653589793" periodicity2="2" k2="2.5564452357481624" phase2="3.141592653589793" periodicity3="3" k3="0.6456854236483743" phase3="0.0" periodicity4="4" k4="0.7314356894933955" phase4="3.141592653589793"/>
43+
<Proper class1="C0" class2="C1" class3="C1" class4="H4" periodicity1="1" k1="0.682134452090223" phase1="3.141592653589793" periodicity2="2" k2="2.3315878182279266" phase2="3.141592653589793" periodicity3="3" k3="1.0665263434207997" phase3="0.0" periodicity4="4" k4="1.1146888113517457" phase4="3.141592653589793"/>
44+
<Proper class1="C1" class2="C0" class3="C0" class4="H3" periodicity1="1" k1="0.6612874747218241" phase1="3.141592653589793" periodicity2="2" k2="0.483419675865326" phase2="3.141592653589793" periodicity3="3" k3="0.7296692710615724" phase3="0.0" periodicity4="4" k4="0.7218410810245874" phase4="3.141592653589793"/>
45+
<Proper class1="C1" class2="C1" class3="S2" class4="C1" periodicity1="1" k1="0.9636998079270306" phase1="3.141592653589793" periodicity2="2" k2="2.0409706090428386" phase2="3.141592653589793" periodicity3="3" k3="0.25436992778068435" phase3="0.0" periodicity4="4" k4="1.7999624251851083" phase4="3.141592653589793"/>
46+
<Proper class1="C1" class2="C1" class3="C1" class4="S2" periodicity1="1" k1="0.7687335799138368" phase1="3.141592653589793" periodicity2="2" k2="1.6338215907587652" phase2="3.141592653589793" periodicity3="3" k3="0.3542618758163248" phase3="0.0" periodicity4="4" k4="4.45242496169517" phase4="3.141592653589793"/>
47+
<Proper class1="C1" class2="C1" class3="C1" class4="H5" periodicity1="1" k1="0.570083219086181" phase1="3.141592653589793" periodicity2="2" k2="2.1815039160847336" phase2="3.141592653589793" periodicity3="3" k3="0.7716853027845768" phase3="0.0" periodicity4="4" k4="2.156847260827534" phase4="3.141592653589793"/>
48+
<Proper class1="C1" class2="C1" class3="C0" class4="H3" periodicity1="1" k1="0.38728187322744817" phase1="3.141592653589793" periodicity2="2" k2="0.9219229460656695" phase2="3.141592653589793" periodicity3="3" k3="0.43900193554126477" phase3="0.0" periodicity4="4" k4="0.34081858108351826" phase4="3.141592653589793"/>
49+
<Proper class1="C1" class2="C1" class3="C1" class4="C1" periodicity1="1" k1="0.5206761509295338" phase1="3.141592653589793" periodicity2="2" k2="2.0487999452612695" phase2="3.141592653589793" periodicity3="3" k3="0.6130560066678546" phase3="0.0" periodicity4="4" k4="0.8629304388917788" phase4="3.141592653589793"/>
50+
<Proper class1="C1" class2="C1" class3="C1" class4="H4" periodicity1="1" k1="0.6412500835144828" phase1="3.141592653589793" periodicity2="2" k2="1.8733197187679993" phase2="3.141592653589793" periodicity3="3" k3="0.7413555842564578" phase3="0.0" periodicity4="4" k4="1.0437038077128085" phase4="3.141592653589793"/>
51+
<Proper class1="C1" class2="S2" class3="C1" class4="C1" periodicity1="1" k1="0.6960290748702487" phase1="3.141592653589793" periodicity2="2" k2="2.088983844149571" phase2="3.141592653589793" periodicity3="3" k3="0.5547735206934491" phase3="0.0" periodicity4="4" k4="3.53922094147389" phase4="3.141592653589793"/>
52+
<Proper class1="C1" class2="S2" class3="C1" class4="H5" periodicity1="1" k1="0.253896535740638" phase1="3.141592653589793" periodicity2="2" k2="0.9487142496471072" phase2="3.141592653589793" periodicity3="3" k3="0.30464962207789564" phase3="0.0" periodicity4="4" k4="1.8754742342372939" phase4="3.141592653589793"/>
53+
<Proper class1="S2" class2="C1" class3="C1" class4="C1" periodicity1="1" k1="0.6110069398915527" phase1="3.141592653589793" periodicity2="2" k2="3.3714306755352688" phase2="3.141592653589793" periodicity3="3" k3="0.8516906779880893" phase3="0.0" periodicity4="4" k4="1.3471516776480432" phase4="3.141592653589793"/>
54+
<Proper class1="S2" class2="C1" class3="C1" class4="H4" periodicity1="1" k1="0.5612513561633545" phase1="3.141592653589793" periodicity2="2" k2="1.8362699384244767" phase2="3.141592653589793" periodicity3="3" k3="0.6686530659273753" phase3="0.0" periodicity4="4" k4="2.0740096712720066" phase4="3.141592653589793"/>
55+
<Proper class1="H3" class2="C0" class3="C0" class4="H3" periodicity1="1" k1="0.7212915252274826" phase1="3.141592653589793" periodicity2="2" k2="0.526992527639806" phase2="3.141592653589793" periodicity3="3" k3="0.795905797795687" phase3="0.0" periodicity4="4" k4="0.7872790249395221" phase4="3.141592653589793"/>
56+
<Proper class1="H4" class2="C1" class3="C1" class4="H5" periodicity1="1" k1="0.7060693950971926" phase1="3.141592653589793" periodicity2="2" k2="2.083876918100669" phase2="3.141592653589793" periodicity3="3" k3="0.8218595483887952" phase3="0.0" periodicity4="4" k4="1.1600202111121225" phase4="3.141592653589793"/>
57+
<Proper class1="S2" class2="C1" class3="C1" class4="S2" periodicity1="1" k1="1.070931195128239" phase1="3.141592653589793" periodicity2="2" k2="1.744053528160295" phase2="3.141592653589793" periodicity3="3" k3="0.7096954547184122" phase3="0.0" periodicity4="4" k4="1.0641796515291302" phase4="3.141592653589793"/>
58+
<Proper class1="C1" class2="C1" class3="C1" class4="C0" periodicity1="1" k1="0.5978682619809318" phase1="3.141592653589793" periodicity2="2" k2="3.6147194548213073" phase2="3.141592653589793" periodicity3="3" k3="0.738388884614829" phase3="0.0" periodicity4="4" k4="0.7256531276883756" phase4="3.141592653589793"/>
59+
<Proper class1="H4" class2="C1" class3="C1" class4="C1" periodicity1="1" k1="0.6977869351472782" phase1="3.141592653589793" periodicity2="2" k2="1.8910739165357562" phase2="3.141592653589793" periodicity3="3" k3="0.7653483712203806" phase3="0.0" periodicity4="4" k4="1.118810556242128" phase4="3.141592653589793"/>
60+
</PeriodicTorsionForce>
61+
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
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<Atom type="C0" charge="-0.03563004732131958" sigma="0.337953176162662" epsilon="0.45538911611061844"/>
63+
<Atom type="C1" charge="-0.16065320372581482" sigma="0.34806468869450646" epsilon="0.3635030558377792"/>
64+
<Atom type="S2" charge="0.06319281458854675" sigma="0.3563594872561357" epsilon="1.046"/>
65+
<Atom type="H3" charge="0.04735146462917328" sigma="0.26445434132681245" epsilon="0.06602135607582665"/>
66+
<Atom type="H4" charge="0.1513296663761139" sigma="0.2572581535063279" epsilon="0.06531785996356952"/>
67+
<Atom type="H5" charge="0.16874316334724426" sigma="0.24536265277299726" epsilon="0.05483968129296432"/>
68+
</NonbondedForce>
69+
</ForceField>

‎Units exercise.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "67081b67-7a25-48f2-8daa-f78434be755d",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Calculating tau for PPS"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"id": "2381633c-98ef-418a-81af-5c1b506f16eb",
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"metadata": {},
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"outputs": [],
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"source": [
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"import numpy"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 43,
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"id": "bd0aacb8-cf68-4620-814f-19804e586e54",
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"metadata": {},
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"outputs": [],
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"source": [
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"sigma = 0.3438e-9 # nm to meters\n",
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"epsilon = 1.7782 * 1000 # kJ to J\n",
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"mass = 68.0 / 1000 # g to kg"
33+
]
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},
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{
36+
"cell_type": "code",
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"execution_count": 24,
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"id": "c96c3a58-5e42-4237-8a87-7bafb8ccabb1",
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"metadata": {},
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"outputs": [],
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"source": [
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"tau = numpy.sqrt((mass * (sigma**2)) / epsilon)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 27,
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"id": "38a6a264-08dd-4566-aa49-b9b590fffeb4",
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"metadata": {},
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"outputs": [
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{
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"data": {
53+
"text/plain": [
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"2.126033119686479e-12"
55+
]
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},
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"execution_count": 27,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"tau"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 28,
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"id": "921fcaf7-bb84-4477-a610-e4066baf5c36",
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"metadata": {},
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"outputs": [
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{
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"data": {
74+
"text/plain": [
75+
"2.1260331196864793e-15"
76+
]
77+
},
78+
"execution_count": 28,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"tau * 0.001 # one time step of 0.001"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "5325480a-21af-4ebe-8004-d6d12d54dd35",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Find the volume of a box with 100000 monomers of PPS and a density of 1.2 g/cm^3"
95+
]
96+
},
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{
98+
"cell_type": "code",
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"execution_count": 2,
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"id": "f564c18d-9a7b-4de1-ae19-2a348c7ab407",
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"metadata": {},
102+
"outputs": [
103+
{
104+
"data": {
105+
"text/plain": [
106+
"9.409941326248203e-18"
107+
]
108+
},
109+
"execution_count": 2,
110+
"metadata": {},
111+
"output_type": "execute_result"
112+
}
113+
],
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"source": [
115+
"mass = 68 / (6.022e23) # g/mol to g of one monomer\n",
116+
"density = 1.2\n",
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"n = 100000\n",
118+
"volume = (n * mass) / density\n",
119+
"volume"
120+
]
121+
},
122+
{
123+
"cell_type": "code",
124+
"execution_count": 5,
125+
"id": "1e07ad36-1b4b-4746-8d98-347a6a6e4e2b",
126+
"metadata": {},
127+
"outputs": [
128+
{
129+
"data": {
130+
"text/plain": [
131+
"2.1111980293376474e-06"
132+
]
133+
},
134+
"execution_count": 5,
135+
"metadata": {},
136+
"output_type": "execute_result"
137+
}
138+
],
139+
"source": [
140+
"L = numpy.cbrt(volume)\n",
141+
"L"
142+
]
143+
},
144+
{
145+
"cell_type": "code",
146+
"execution_count": 6,
147+
"id": "7eaa4cdd-3b7f-4c0f-959a-ee16e7edf3e2",
148+
"metadata": {},
149+
"outputs": [],
150+
"source": [
151+
"# given box with length of 10nm, how many monomers are inside the box at that density?"
152+
]
153+
},
154+
{
155+
"cell_type": "code",
156+
"execution_count": 7,
157+
"id": "256f63cf-9882-4f23-95d5-de5851cc9b03",
158+
"metadata": {},
159+
"outputs": [
160+
{
161+
"data": {
162+
"text/plain": [
163+
"1.1999999999999998e-18"
164+
]
165+
},
166+
"execution_count": 7,
167+
"metadata": {},
168+
"output_type": "execute_result"
169+
}
170+
],
171+
"source": [
172+
"length = 1e-6\n",
173+
"m = (length**3) * density\n",
174+
"m"
175+
]
176+
},
177+
{
178+
"cell_type": "code",
179+
"execution_count": 8,
180+
"id": "b580cb6a-5ced-44d8-986a-9a04f0c46e39",
181+
"metadata": {},
182+
"outputs": [
183+
{
184+
"data": {
185+
"text/plain": [
186+
"10627.058823529409"
187+
]
188+
},
189+
"execution_count": 8,
190+
"metadata": {},
191+
"output_type": "execute_result"
192+
}
193+
],
194+
"source": [
195+
"monomers = m / mass\n",
196+
"monomers"
197+
]
198+
},
199+
{
200+
"cell_type": "code",
201+
"execution_count": null,
202+
"id": "b88b8ea7-f897-46d9-928b-e6b15068e836",
203+
"metadata": {},
204+
"outputs": [],
205+
"source": [
206+
"# what is the change in box length per step with 20Hz and 38micron amplitude"
207+
]
208+
},
209+
{
210+
"cell_type": "code",
211+
"execution_count": null,
212+
"id": "40eb2918-b7dc-4e07-983b-cd5faa3e0b62",
213+
"metadata": {},
214+
"outputs": [],
215+
"source": [
216+
"frequency = 20 # 1/s\n",
217+
"amplitude = 3.8e-5"
218+
]
219+
}
220+
],
221+
"metadata": {
222+
"kernelspec": {
223+
"display_name": "Python 3 (ipykernel)",
224+
"language": "python",
225+
"name": "python3"
226+
},
227+
"language_info": {
228+
"codemirror_mode": {
229+
"name": "ipython",
230+
"version": 3
231+
},
232+
"file_extension": ".py",
233+
"mimetype": "text/x-python",
234+
"name": "python",
235+
"nbconvert_exporter": "python",
236+
"pygments_lexer": "ipython3",
237+
"version": "3.11.9"
238+
}
239+
},
240+
"nbformat": 4,
241+
"nbformat_minor": 5
242+
}

‎flowermd/base/system.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -675,7 +675,7 @@ def __init__(
675675
self.fix_orientation = fix_orientation
676676
super(Pack, self).__init__(molecules=molecules, base_units=base_units)
677677

678-
def _build_system(self,**kwargs):
678+
def _build_system(self, **kwargs):
679679
mass_density = u.Unit("kg") / u.Unit("m**3")
680680
number_density = u.Unit("m**-3")
681681
if self.density.units.dimensions == mass_density.dimensions:
@@ -702,7 +702,7 @@ def _build_system(self,**kwargs):
702702
seed=self.seed,
703703
edge=self.edge,
704704
fix_orientation=self.fix_orientation,
705-
**kwargs
705+
**kwargs,
706706
)
707707
return system
708708

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