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@StephMcCallum
StephMcCallum committed Jan 24, 2025
2 parents 8c3336f + 0035b1f commit 5fa9efd
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65 changes: 65 additions & 0 deletions P3HT.mol2
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@<TRIPOS>MOLECULE
RES
27 27 1 0 1
SMALL
NO_CHARGES
@<TRIPOS>CRYSIN
13.8222 9.4717 9.3109 90.0000 90.0000 90.0000 1 1
@<TRIPOS>ATOM
1 C0 14.1713 10.6638 10.2575 C0 1 RES
2 C0 12.7816 10.5396 9.6397 C0 1 RES
3 C0 11.8555 9.6942 10.5225 C0 1 RES
4 C0 10.4652 9.5693 9.8894 C0 1 RES
5 C0 9.5345 8.7093 10.7585 C0 1 RES
6 C0 8.1488 8.5349 10.1180 C0 1 RES
7 C1 7.4178 9.8420 9.9706 C1 1 RES
8 C1 7.0527 10.6406 11.0504 C1 1 RES
9 S2 6.2624 11.9995 10.4564 S2 1 RES
10 C1 6.3741 11.5898 8.8302 C1 1 RES
11 C1 7.0354 10.3740 8.7296 C1 1 RES
12 H3 14.8183 11.2776 9.5959 H3 1 RES
13 H3 14.6325 9.6595 10.3735 H3 1 RES
14 H3 14.1093 11.1550 11.2515 H3 1 RES
15 H3 12.8767 10.0661 8.6379 H3 1 RES
16 H3 12.3520 11.5574 9.5139 H3 1 RES
17 H3 12.2944 8.6797 10.6472 H3 1 RES
18 H3 11.7630 10.1704 11.5235 H3 1 RES
19 H3 10.0306 10.5856 9.7667 H3 1 RES
20 H3 10.5621 9.0987 8.8861 H3 1 RES
21 H3 9.9875 7.7008 10.8798 H3 1 RES
22 H3 9.4290 9.1641 11.7676 H3 1 RES
23 H3 7.5352 7.8577 10.7499 H3 1 RES
24 H3 8.2742 8.0520 9.1238 H3 1 RES
25 H4 7.2362 9.8904 7.7826 H4 1 RES
26 H5 7.2416 10.4260 12.0935 H5 1 RES
27 H5 5.9961 12.1726 8.0013 H5 1 RES
@<TRIPOS>BOND
1 1 2 1
2 1 12 1
3 1 13 1
4 1 14 1
5 2 3 1
6 2 15 1
7 2 16 1
8 3 4 1
9 3 17 1
10 3 18 1
11 4 5 1
12 4 19 1
13 4 20 1
14 5 6 1
15 5 21 1
16 5 22 1
17 6 7 1
18 6 23 1
19 6 24 1
20 7 8 1
21 7 11 1
22 8 9 1
23 8 26 1
24 9 10 1
25 10 11 1
26 10 27 1
27 11 25 1
@<TRIPOS>SUBSTRUCTURE
1 RES 1 RESIDUE 0 **** ROOT 0
69 changes: 69 additions & 0 deletions P3HT.xml
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<ForceField name="" version="" combining_rule="geometric">
<AtomTypes>
<Type name="H5" class="H5" element="_H5" mass="1.008" def="_H5" desc=""/>
<Type name="H3" class="H3" element="_H3" mass="1.008" def="_H3" desc=""/>
<Type name="H4" class="H4" element="_H4" mass="1.008" def="_H4" desc=""/>
<Type name="S2" class="S2" element="_S2" mass="32.06" def="_S2" desc=""/>
<Type name="C0" class="C0" element="_C0" mass="12.011" def="_C0" desc=""/>
<Type name="C1" class="C1" element="_C1" mass="12.011" def="_C1" desc=""/>
</AtomTypes>
<HarmonicBondForce>
<Bond class1="C0" class2="C0" length="0.15393138859485156" k="216071.5673604569"/>
<Bond class1="C0" class2="H3" length="0.10976204613301968" k="306243.2994478932"/>
<Bond class1="C0" class2="C1" length="0.15021762614242648" k="245043.09124482484"/>
<Bond class1="C1" class2="C1" length="0.13696133519685275" k="417404.23786464764"/>
<Bond class1="C1" class2="S2" length="0.17644359746123384" k="146619.58148765477"/>
<Bond class1="C1" class2="H5" length="0.10847683421363911" k="342520.45189188817"/>
<Bond class1="S2" class2="C1" length="0.17456724887079533" k="155523.3472930218"/>
<Bond class1="C1" class2="H4" length="0.10863386001736958" k="335143.64070747164"/>
</HarmonicBondForce>
<HarmonicAngleForce>
<Angle class1="C0" class2="C0" class3="C0" angle="1.971023440361023" k="571.7145128119677"/>
<Angle class1="C0" class2="C0" class3="H3" angle="1.919396162033081" k="400.7807950494681"/>
<Angle class1="C0" class2="C0" class3="C1" angle="1.9725769758224487" k="567.2166987593794"/>
<Angle class1="C0" class2="C1" class3="C1" angle="2.387712240219116" k="370.1760901705978"/>
<Angle class1="C1" class2="C0" class3="H3" angle="1.916161298751831" k="419.6637425240785"/>
<Angle class1="C1" class2="C1" class3="S2" angle="2.26436710357666" k="600.522063868667"/>
<Angle class1="C1" class2="C1" class3="H5" angle="2.385676145553589" k="242.64219357507048"/>
<Angle class1="C1" class2="C1" class3="C1" angle="2.221386194229126" k="622.0677222701529"/>
<Angle class1="C1" class2="C1" class3="H4" angle="2.2988548278808594" k="253.7424039841016"/>
<Angle class1="C1" class2="S2" class3="C1" angle="1.749892234802246" k="1116.8353273914954"/>
<Angle class1="S2" class2="C1" class3="H5" angle="2.220374345779419" k="269.41800934151877"/>
<Angle class1="S2" class2="C1" class3="C1" angle="2.220290422439575" k="647.3334296165826"/>
<Angle class1="H3" class2="C0" class3="H3" angle="1.889668583869934" k="334.4416957736681"/>
</HarmonicAngleForce>
<PeriodicTorsionForce>
<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"/>
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<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
<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"/>
</PeriodicTorsionForce>
<NonbondedForce coulomb14scale="1.0" lj14scale="1.0">
<Atom type="C0" charge="-0.03563004732131958" sigma="0.337953176162662" epsilon="0.45538911611061844"/>
<Atom type="C1" charge="-0.16065320372581482" sigma="0.34806468869450646" epsilon="0.3635030558377792"/>
<Atom type="S2" charge="0.06319281458854675" sigma="0.3563594872561357" epsilon="1.046"/>
<Atom type="H3" charge="0.04735146462917328" sigma="0.26445434132681245" epsilon="0.06602135607582665"/>
<Atom type="H4" charge="0.1513296663761139" sigma="0.2572581535063279" epsilon="0.06531785996356952"/>
<Atom type="H5" charge="0.16874316334724426" sigma="0.24536265277299726" epsilon="0.05483968129296432"/>
</NonbondedForce>
</ForceField>
242 changes: 242 additions & 0 deletions Units exercise.ipynb
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{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "67081b67-7a25-48f2-8daa-f78434be755d",
"metadata": {},
"outputs": [],
"source": [
"# Calculating tau for PPS"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "2381633c-98ef-418a-81af-5c1b506f16eb",
"metadata": {},
"outputs": [],
"source": [
"import numpy"
]
},
{
"cell_type": "code",
"execution_count": 43,
"id": "bd0aacb8-cf68-4620-814f-19804e586e54",
"metadata": {},
"outputs": [],
"source": [
"sigma = 0.3438e-9 # nm to meters\n",
"epsilon = 1.7782 * 1000 # kJ to J\n",
"mass = 68.0 / 1000 # g to kg"
]
},
{
"cell_type": "code",
"execution_count": 24,
"id": "c96c3a58-5e42-4237-8a87-7bafb8ccabb1",
"metadata": {},
"outputs": [],
"source": [
"tau = numpy.sqrt((mass * (sigma**2)) / epsilon)"
]
},
{
"cell_type": "code",
"execution_count": 27,
"id": "38a6a264-08dd-4566-aa49-b9b590fffeb4",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"2.126033119686479e-12"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"tau"
]
},
{
"cell_type": "code",
"execution_count": 28,
"id": "921fcaf7-bb84-4477-a610-e4066baf5c36",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"2.1260331196864793e-15"
]
},
"execution_count": 28,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"tau * 0.001 # one time step of 0.001"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "5325480a-21af-4ebe-8004-d6d12d54dd35",
"metadata": {},
"outputs": [],
"source": [
"# Find the volume of a box with 100000 monomers of PPS and a density of 1.2 g/cm^3"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "f564c18d-9a7b-4de1-ae19-2a348c7ab407",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"9.409941326248203e-18"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mass = 68 / (6.022e23) # g/mol to g of one monomer\n",
"density = 1.2\n",
"n = 100000\n",
"volume = (n * mass) / density\n",
"volume"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "1e07ad36-1b4b-4746-8d98-347a6a6e4e2b",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"2.1111980293376474e-06"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"L = numpy.cbrt(volume)\n",
"L"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "7eaa4cdd-3b7f-4c0f-959a-ee16e7edf3e2",
"metadata": {},
"outputs": [],
"source": [
"# given box with length of 10nm, how many monomers are inside the box at that density?"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "256f63cf-9882-4f23-95d5-de5851cc9b03",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"1.1999999999999998e-18"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"length = 1e-6\n",
"m = (length**3) * density\n",
"m"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "b580cb6a-5ced-44d8-986a-9a04f0c46e39",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"10627.058823529409"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"monomers = m / mass\n",
"monomers"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b88b8ea7-f897-46d9-928b-e6b15068e836",
"metadata": {},
"outputs": [],
"source": [
"# what is the change in box length per step with 20Hz and 38micron amplitude"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "40eb2918-b7dc-4e07-983b-cd5faa3e0b62",
"metadata": {},
"outputs": [],
"source": [
"frequency = 20 # 1/s\n",
"amplitude = 3.8e-5"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.9"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
4 changes: 2 additions & 2 deletions flowermd/base/system.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -675,7 +675,7 @@ def __init__(
self.fix_orientation = fix_orientation
super(Pack, self).__init__(molecules=molecules, base_units=base_units)

def _build_system(self,**kwargs):
def _build_system(self, **kwargs):
mass_density = u.Unit("kg") / u.Unit("m**3")
number_density = u.Unit("m**-3")
if self.density.units.dimensions == mass_density.dimensions:
Expand All @@ -702,7 +702,7 @@ def _build_system(self,**kwargs):
seed=self.seed,
edge=self.edge,
fix_orientation=self.fix_orientation,
**kwargs
**kwargs,
)
return system

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