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Cartesian to normal mode coordinates
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cartesian2modes.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "a3d9af65",
"metadata": {},
"outputs": [],
"source": [
"using LinearAlgebra, Printf"
]
},
{
"cell_type": "markdown",
"id": "75f46b68",
"metadata": {},
"source": [
"Define the molecule type."
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "75192673",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"numberofatoms (generic function with 1 method)"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"abstract type AbstractMolecule end\n",
"mutable struct ExampleMolecule <: AbstractMolecule\n",
" attr::Dict{Symbol, Any}\n",
"end\n",
"\n",
"Base.getproperty(m::AbstractMolecule, s::Symbol)=getfield(m,:attr)[s]\n",
"Base.setproperty!(m::AbstractMolecule, s::Symbol, x)=getfield(m,:attr)[s]=x\n",
"Base.propertynames(m::AbstractMolecule)=Tuple(keys(getfield(m,:attr)))\n",
"numberofatoms(m::AbstractMolecule)=length(m.elements)"
]
},
{
"cell_type": "markdown",
"id": "2497c39b",
"metadata": {},
"source": [
"Print function."
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "63b7f51b",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"toxyz (generic function with 1 method)"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"const ang=1.8897261254578281\n",
"export toxyz, ang\n",
"function toxyz(m::AbstractMolecule)\n",
" res=\"\"\n",
" natoms = length(m.elements)\n",
" res *= \"$natoms \\n\\n\"\n",
" for i in 1:natoms\n",
" res *= Printf.@sprintf \"%5s %16.8f %16.8f %16.8f\\n\" m.elements[i] m.xyz[1,i]/ang m.xyz[2,i]/ang m.xyz[3,i]/ang\n",
" end\n",
" res\n",
"end"
]
},
{
"cell_type": "markdown",
"id": "ee94dfbf",
"metadata": {},
"source": [
"Deform the molecule along normal mode."
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "4e70a4a7",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"deform (generic function with 1 method)"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"function deform!(m::AbstractMolecule, Q)\n",
" xyz=m.xyz\n",
" for k in keys(Q) # Both Array and Dict can have keys\n",
" xyz+=reshape(m.normalmodes[:,k]*Q[k],3,:)\n",
" end\n",
" m.xyz=xyz\n",
" m\n",
"end\n",
"function deform(m::AbstractMolecule, Q)\n",
" mm=deepcopy(m)\n",
" deform!(mm,Q)\n",
"end"
]
},
{
"cell_type": "markdown",
"id": "3aced1d7",
"metadata": {},
"source": [
"Rotation"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "f7052314",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"rotate (generic function with 1 method)"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"function rotate(origin::AbstractMolecule, r)\n",
" res=typeof(origin)(Dict(:xyz=>origin.xyz, :elements=>origin.elements, :masses=>origin.masses))\n",
" res.xyz=r*res.xyz\n",
" res\n",
"end"
]
},
{
"cell_type": "markdown",
"id": "99dcf7cb",
"metadata": {},
"source": [
"Now we prepare the functions. The Kabsch's algorithm (see Wikipedia.)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "803bdeaa",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Kabsch (generic function with 1 method)"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"function Kabsch(origin,rotated)\n",
" H=rotated*origin'\n",
" U,S,V=LinearAlgebra.svd(H)\n",
" d=sign(det(V*U'))\n",
" R=U*diagm([1.0, 1.0, d])*V'\n",
"end"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "85b6a60d",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Kabsch (generic function with 2 methods)"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"function Kabsch(origin::AbstractMolecule, rotated::AbstractMolecule) where T<:AbstractMolecule\n",
" return Kabsch(origin.xyz, rotated.xyz)\n",
"end"
]
},
{
"cell_type": "markdown",
"id": "6527d06f",
"metadata": {},
"source": [
"RMSD"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "f353d227",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"rmsd (generic function with 1 method)"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"function rmsd(origin::AbstractMolecule, rotated::AbstractMolecule) where T<:AbstractMolecule\n",
" return norm(origin.xyz-rotated.xyz)\n",
"end"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "e52a61de",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"normalmodescomponemts (generic function with 1 method)"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"function normalmodescomponemts(origin, deformed)\n",
" δ=reshape((deformed.xyz-origin.xyz),(3*numberofatoms(origin),))\n",
" mw=[sqrt(origin.masses[i]) for i in 1:numberofatoms(origin) for j in 1:3]\n",
" (mw.*δ)'*origin.massweightednormalmodes\n",
"end"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "36de4c9f",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"findvibrationcoordinates (generic function with 1 method)"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"function findvibrationcoordinates(origin, deformed)\n",
" m0=deepcopy(origin)\n",
" # m1=deepcopy(deformed)\n",
" r=zeros(3,3)\n",
" comp=zeros(numberofatoms(origin)*3)\n",
" for i in 1:50\n",
" r.=Kabsch(m0, deformed) # rot mat\n",
" m1=rotate(deformed, r')\n",
" if rmsd(m0,m1) ≈ 0.0\n",
" break\n",
" end\n",
" comp.=reshape(normalmodescomponemts(origin, m1) |> Matrix, length(comp))\n",
" comp[1:6] .= 0.0\n",
" m0=deform(origin, comp)\n",
" end\n",
" return r, comp\n",
"end"
]
},
{
"cell_type": "markdown",
"id": "87ff4c5e",
"metadata": {},
"source": [
"We take benzene as an example. "
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "cdd60270",
"metadata": {},
"outputs": [],
"source": [
"d=Dict()\n",
"d[:xyz] = [1.370141055623905e-5 2.4393300524131725e-5 -2.2660231413381045 -4.034278655742172 -2.2660368167521896 -4.034303073640448 -1.3700315458456184e-5 -2.4393043784447153e-5 2.266023114234351 4.034278680755381 2.2660368428488176 4.0343030473230455; 2.61658611892533 4.65839790928417 1.3083048564084279 2.329220093828624 -1.308281123733191 -2.329177843236 -2.616586130127392 -4.6583978908172305 -1.3083048512129214 -2.32922008921674 1.3082811271226484 2.3291778513185175; -4.5668038740802804e-6 -8.130438308776296e-6 5.626534352202108e-6 1.0017112750425859e-5 1.0193337950830708e-5 1.8147551312873786e-5 4.56680398458106e-6 8.130438381482553e-6 -5.626534355084896e-6 -1.0017112998973042e-5 -1.01933380481998e-5 -1.814755125906479e-5]\n",
"d[:frequencies] = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 353.0346094198637, 373.0183109129092, 579.3271598516922, 579.3361470629426, 653.4029959261279, 695.5357511189003, 882.3136303334982, 890.7184426825697, 928.6185691759343, 934.6036980046986, 940.3179197212983, 957.3435192206359, 1067.2938704152866, 1090.6044196624807, 1090.6362560860425, 1176.1206885646288, 1198.3690472562384, 1198.3893714619041, 1304.3522925356915, 1319.9835715178845, 1460.7337200108036, 1461.030395086078, 1600.5152369166942, 1600.5220374615758, 3068.45964758506, 3072.1099118560182, 3072.1525771606634, 3084.252406352897, 3084.2963741776657, 3092.658131777928]\n",
"d[:elements] = Any[\"C\", \"H\", \"C\", \"H\", \"C\", \"H\", \"C\", \"H\", \"C\", \"H\", \"C\", \"H\"]\n",
"d[:normalmodes] = [-0.11319364146658135 0.0 0.0 0.0 -2.5850863007902734e-7 -0.10473280069768069 -3.011576410278993e-7 2.9233999216225573e-7 -0.05972387026327071 -0.005639368156170343 1.0912063811458538e-6 4.267943374186421e-7 1.6801874776533675e-7 1.0014522358279775e-7 2.012715699768969e-7 7.635237549001588e-8 9.712714090401178e-8 7.604530755797708e-7 -4.504876794000749e-6 -0.04943115233908801 -0.010862383406644902 0.00237702414009375 0.03931519176468107 -0.013285479296870826 0.05408106778744616 0.11780210191326929 0.00023295223603703622 -0.11139506163026795 -0.141600598813222 0.04899050994698945 -7.10629470101745e-7 0.0010088929329515647 0.00043989244268631187 0.000280416657953161 0.0006787182459555704 1.708254307642705e-6; 0.0 -0.11319364146658135 0.0 2.5850862605763344e-7 1.6425306279526277e-16 5.484189574747748e-7 -4.8106277893369044e-8 3.684633317096965e-7 -0.013897301966170554 0.14717777625220582 6.88148508223768e-8 -4.408440022520199e-8 -1.329156806387778e-7 -7.673255100017039e-7 -4.896056451719539e-7 -1.4211446424515583e-6 -9.421399653532053e-8 -0.11394893685646973 0.11274149745632486 0.017655756050878164 -0.08034805268901256 7.328088496099873e-6 -0.0031316075652744256 -0.009267831865743778 9.971636599414318e-6 -3.565793709242793e-6 -0.07736872080122194 -0.0001656397197812293 0.02034202743149085 0.05879549086441988 0.030128671437787337 0.017660119911206126 -0.040569240302082726 0.04345975118469603 -0.017874336394970648 0.03431447819174405; 0.0 0.0 -0.11319364146658135 0.14811454601848575 -7.754873358071593e-7 -3.6558640877822526e-7 -0.09084712098510173 0.10672898763976468 1.3798775785438016e-6 -1.828071542175284e-8 0.11009905144250104 0.030361254789249777 0.07399185381154387 0.012453738808902309 0.08991572158175357 0.0142442302059204 0.044464658796659 -2.74384246694781e-7 8.179159306408159e-8 6.659693021930428e-8 1.4146728748646188e-8 -8.733780835368839e-9 -1.1604781645613452e-7 1.0465726933522798e-7 -1.7779136208677715e-7 -4.116386005587309e-7 4.000587996715028e-8 3.4740784717952745e-7 4.792260230307363e-7 -2.194337288187906e-7 -7.505282819456539e-8 -2.5961554399106465e-9 1.0048194653883641e-7 -9.65185389676017e-8 -1.670488369089418e-8 -5.370913176183876e-8; -0.1131936414665813 0.0 0.0 0.0 -4.602318223425772e-7 -0.18645939312860596 -6.952697847861604e-7 7.516085205556293e-7 0.08615856990067376 0.008138015350809092 -4.0069133060237715e-7 -7.872473454764005e-7 -1.7224231988730721e-6 -1.2270429938217193e-7 -2.2232821198985097e-6 -7.26405262030151e-8 -1.3688052063535373e-6 -8.356985901177083e-6 2.246207494318726e-5 -0.45031970848702885 -0.098996347426387 -0.4066221446573035 0.5266189984437923 -0.177973179479002 -0.36146307846690573 0.008218708681702398 -0.000677925741382254 0.3245097200465926 0.11261691266528605 -0.03895239299836196 -3.629377312924938e-6 -0.0017841168659206506 -0.0007743231226340477 -0.00034380990494800037 -0.0008380346048459789 3.9453745429596656e-7; 0.0 -0.1131936414665813 0.0 4.602318151600923e-7 3.31771375987615e-16 9.763774604095047e-7 1.6526840738457277e-7 7.099602052430992e-8 -0.013366235228354445 0.14154400952538349 -2.2153630661894802e-7 -5.881739084584726e-7 -1.0947429679629676e-6 -9.902160026044835e-7 -6.268055741717497e-7 -1.3195851387308185e-6 -1.8928758182093097e-7 -0.10395881466444937 0.11843012046127273 0.017918559580124824 -0.08154525476306901 6.720643947970922e-6 -0.0026524255933780367 -0.007850969764094084 1.2973467945164223e-5 -4.237658709607271e-6 -0.08073518888963167 -0.00017706087010321917 0.01802835315423673 0.052112587878530396 -0.3931919733429744 -0.22136696821263308 0.5084189020846676 -0.5102693531927635 0.2098277635924631 -0.3889505929771131; 0.0 0.0 -0.1131936414665813 0.26369340054072865 -1.3806385537653817e-6 -6.508660083435814e-7 -0.20045811488183682 0.23257671017705722 2.918168239762718e-6 1.2879691186976179e-7 0.14553664563161667 -0.39681503369382676 -0.4965084938721388 -0.0754834080537639 -0.47677982439082484 -0.06517907447699145 -0.3913879191862286 3.100668030694579e-6 -2.1103684546506927e-6 9.76621838472741e-7 1.0258529101365689e-6 1.405873224727441e-6 -1.786337141630278e-6 3.924191029051166e-7 1.8298906229700635e-6 -2.9279397955945507e-9 4.744832230612272e-7 -1.7825146140985647e-6 -4.4635299059538736e-7 -2.1690494975324538e-7 -1.906719286836328e-8 1.1193335606217567e-6 6.221960764349815e-9 3.404728090007704e-8 -7.918624489260824e-7 6.366592764483426e-7; 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0.0 -0.1131936414665813 0.0 5.670289747115729e-7 3.635863904272734e-16 0.16147808091316182 8.756317005379679e-7 8.289931020488539e-8 -0.033468114619566426 0.09774317628193845 3.4819767432759506e-7 -1.6632554370780557e-7 9.990426386297285e-7 1.7216778083023608e-7 4.6804276491487914e-7 2.059375758548953e-6 -1.3121286952358943e-6 0.05206845902975046 -0.05942850302350536 -0.30010132642243575 0.2668105007074916 0.3520674064831736 0.36428536077195584 0.3147526560713482 0.31291122282989664 -0.007064529083623338 -0.2636849021273775 0.105063443518592 0.046754348188928124 -0.09620587257170886 0.1967822901572927 -0.275858619875196 0.029251259041685882 -0.21804555078304122 -0.16884303584079857 0.19430959673887768; 0.0 0.0 -0.1131936414665813 -0.13184789661468022 -0.22836449391395336 6.07266268081453e-7 0.3136778861025645 0.048692156067998656 3.9970761705181905e-7 3.04693132257142e-7 0.14673894952901598 -0.38006020289345366 0.35111154384607124 -0.3295769237766823 0.17266672785511342 0.4563780579312128 -0.41611404449525136 -6.509652184873186e-6 -2.6532257946752543e-6 -2.5723732785768384e-7 -8.450068006727576e-7 -1.3330197000917022e-6 -1.3958391306012554e-6 -9.395013969641181e-7 -1.6758223266290005e-6 2.3868646929083897e-8 1.4152842135643497e-6 -1.3599555336645266e-6 1.3849910808260347e-7 7.573102812429508e-7 -1.719565187582903e-8 -4.4967002294571075e-7 9.867865050457348e-7 7.694290331446566e-8 -7.802658517799742e-7 7.829742545623626e-7; -0.1131936414665813 0.0 0.0 0.0 -5.770043836861035e-7 -0.05236592273840526 -2.582986894745286e-7 -7.463327607721872e-7 -0.08699425433334403 -0.09859609815327945 8.132169753577522e-7 -4.113505837674264e-7 -3.611956479582998e-7 -5.83792670997208e-7 4.3565495132905846e-7 1.3793551354551767e-6 -1.1364557418519826e-7 0.09866410661848371 0.09762549647495695 0.060292375381612084 -0.04567496200742937 -0.0011833415582742166 0.0042717020123580465 0.02205388172118053 0.026988885591370138 -0.05891294567672834 -0.08178710086970893 0.02999260037600158 0.09192189563712576 0.008364685759443472 -0.026055801849113165 0.022281889789358078 0.03113797503406301 0.005746145043674872 -0.04031323522467921 0.029763309116265055; 0.0 -0.1131936414665813 0.0 5.770043747087368e-7 3.699913095984752e-16 0.09070153789937453 -1.8425275809656202e-7 -2.922761036179091e-7 -0.09034008043932805 -0.00046820388020841244 9.562605720851416e-7 -2.1180053808652875e-7 -3.052463480430997e-7 -4.502860621103921e-7 3.5191288718685856e-7 7.497038920166064e-7 -6.592458278443432e-11 0.05697052194869926 0.056390896459497325 0.05249328138657169 0.02929033956089603 0.0020376984064102723 0.011878886512673006 -0.03423878382003357 -0.046788698376687816 0.10206356763714139 0.06402083610145906 0.08182559541581742 -0.07771060670937356 -0.10849903654830434 -0.01504482644772992 0.013886581973044277 0.017224144639085195 0.002482209784535831 -0.023388768556691072 0.017185399051387946; 0.0 0.0 -0.1131936414665813 0.07405659756687477 -0.1282713459762744 -2.4489630633844198e-8 -0.04740342318196559 -0.13220903990736227 -1.0243057968996643e-6 8.908933077335535e-8 -0.10963254339430775 0.034916420854831404 0.02243196590361261 0.07764938216335612 -0.05617340944564381 0.06894209262931669 -0.0343040162608134 -1.27415205098913e-6 1.5755966002842007e-7 -4.9399924547130657e-8 1.6037646174128563e-7 -1.9757700718095207e-9 -1.1876172527128936e-7 -3.865210270421792e-8 -1.6293939462578667e-7 2.813612388533268e-8 1.7382117874653417e-7 -1.0206245255015477e-7 -1.6959321022519297e-7 8.49143386177727e-8 1.698404938500022e-7 -1.3160769321887786e-7 -1.68840167253894e-7 -3.223235269127859e-8 1.8730136229976603e-7 -1.1934552727551615e-7; -0.1131936414665813 0.0 0.0 0.0 -1.0272608030987008e-6 -0.09322885187100609 -2.5704003836416945e-8 -1.2767179353528766e-7 -0.12541250323873052 -0.03603367481984645 1.913863964434266e-6 -1.5117167125348114e-6 -1.4215741375120062e-6 -2.540423501670176e-6 5.091754264819334e-7 9.405518165083321e-7 -1.652183735057918e-9 0.08996595880301292 0.10248602507316645 -0.0007735063534576496 -0.241673604559492 0.20328765864782525 -0.047491611903131156 0.27401532948075424 -0.18070288647168806 -0.004052463321228196 0.10523311605198118 0.14192840670545673 -0.013842426814468296 -0.07510900540049839 0.340104904887486 -0.284044549727628 -0.38673450618755634 -0.06365548482937607 0.4738389038979542 -0.33737619495416826; 0.0 -0.1131936414665813 0.0 1.0272607871158265e-6 6.590880805166292e-16 0.16147905622059924 7.986166974237762e-9 1.513147108825087e-7 -0.014576603942703147 -0.10227571195281408 2.567331266559442e-7 -6.819276304297585e-7 2.227329152546614e-7 -1.316707087491925e-6 6.411763320427717e-7 6.344569345275049e-7 -3.607074117218872e-7 0.05205764023147566 0.05936506408162268 0.16055912567275032 0.36802443004306873 -0.35210178516835694 0.09869569362967971 -0.47119236907653833 0.3129540754021472 0.007042743723360511 -0.2632707674116471 -0.10617373984524163 0.0962188920905851 0.046739620758475736 0.19636593179165412 -0.16579326209832695 -0.22193809070439438 -0.03573509651319199 0.27373082099517426 -0.19481919550508947; 0.0 0.0 -0.1131936414665813 0.1318455056950484 -0.2283658730392661 -4.359974634633153e-8 -0.09698163352206714 -0.2956682144530896 -4.69793618032389e-7 1.4904660030092786e-7 -0.14865821550166192 -0.3945496523267715 -0.14837144228389174 -0.5271239121623343 0.30278889452913244 -0.3730019247689357 0.32343412928549886 1.6235445038658487e-6 -4.411469880677774e-6 -1.8611853700030385e-6 6.448694030938542e-7 -7.774813726636115e-8 3.966904713168369e-7 -2.9669464136496803e-8 4.4906539916463194e-7 5.939718661997159e-10 5.375859740422538e-7 -9.742064400001692e-7 -3.3921502739531256e-7 5.83283461051429e-7 5.4368279622252254e-8 5.397719227584626e-7 8.389010661360923e-7 4.3821602694649363e-8 -7.397489706573001e-7 1.4211594479478532e-6]\n",
"d[:masses] = [12.0, 1.00782503223, 12.0, 1.00782503223, 12.0, 1.00782503223, 12.0, 1.00782503223, 12.0, 1.00782503223, 12.0, 1.00782503223]\n",
"mw=[sqrt(d[:masses][i]) for i in 1:12 for j in 1:3]\n",
"d[:massweightednormalmodes] = d[:normalmodes].*mw\n",
"c6h6=ExampleMolecule(d);"
]
},
{
"cell_type": "markdown",
"id": "4ce226b3",
"metadata": {},
"source": [
"Randomly generated rotation matrix."
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "bae1196e",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"3×3 Matrix{Float64}:\n",
" 0.946584 0.224051 0.231904\n",
" 0.322222 -0.629795 -0.706775\n",
" -0.012302 0.743746 -0.668349"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"r=[0.946584142561884 0.22405148994369173 0.231903839779325; 0.32222216225304745 -0.6297953484751353 -0.7067748560836424; -0.012301999973736447 0.743746427818712 -0.6683486454714722]"
]
},
{
"cell_type": "markdown",
"id": "5b9c673f",
"metadata": {},
"source": [
"Print some basic info of the molecule."
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "44ecf5d6",
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"12 \n",
"\n",
" C 0.00000725 1.38463774 -0.00000242\n",
" H 0.00001291 2.46511801 -0.00000430\n",
" C -1.19912781 0.69232511 0.00000298\n",
" H -2.13484833 1.23257019 0.00000530\n",
" C -1.19913504 -0.69231256 0.00000539\n",
" H -2.13486125 -1.23254783 0.00000960\n",
" C -0.00000725 -1.38463775 0.00000242\n",
" H -0.00001291 -2.46511800 0.00000430\n",
" C 1.19912779 -0.69232511 -0.00000298\n",
" H 2.13484834 -1.23257019 -0.00000530\n",
" C 1.19913506 0.69231256 -0.00000539\n",
" H 2.13486123 1.23254784 -0.00000960\n",
"\n"
]
}
],
"source": [
"toxyz(c6h6) |> println;"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "51502b29",
"metadata": {
"scrolled": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"c6h6.frequencies = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 353.0346094198637, 373.0183109129092, 579.3271598516922, 579.3361470629426, 653.4029959261279, 695.5357511189003, 882.3136303334982, 890.7184426825697, 928.6185691759343, 934.6036980046986, 940.3179197212983, 957.3435192206359, 1067.2938704152866, 1090.6044196624807, 1090.6362560860425, 1176.1206885646288, 1198.3690472562384, 1198.3893714619041, 1304.3522925356915, 1319.9835715178845, 1460.7337200108036, 1461.030395086078, 1600.5152369166942, 1600.5220374615758, 3068.45964758506, 3072.1099118560182, 3072.1525771606634, 3084.252406352897, 3084.2963741776657, 3092.658131777928]\n"
]
}
],
"source": [
"@show c6h6.frequencies;"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "664e81d2",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"ExampleMolecule(Dict{Symbol, Any}(:xyz => [0.5943066687034527 0.8741504920141104 … 2.482473287311426 3.5819921174647953; -1.688000614375677 -2.430660318793785 … -0.06461450830863756 -0.07974604907336512; 2.0001106815024965 2.89411390818984 … 0.9905554102179726 1.4592439443449428], :elements => Any[\"C\", \"H\", \"C\", \"H\", \"C\", \"H\", \"C\", \"H\", \"C\", \"H\", \"C\", \"H\"], :masses => [12.0, 1.00782503223, 12.0, 1.00782503223, 12.0, 1.00782503223, 12.0, 1.00782503223, 12.0, 1.00782503223, 12.0, 1.00782503223]))"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"deformed=rotate(deform(c6h6,Dict(7=>0.3, 8=>0.2, 9=>0.1, 36=>2.0)), r)"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "add79454",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" 1.453785 seconds (3.67 M allocations: 220.455 MiB, 9.03% gc time, 99.49% compilation time)\n"
]
},
{
"data": {
"text/plain": [
"([0.9465841425618841 0.22405148994369173 0.231903839779325; 0.32222216225304745 -0.6297953484751354 -0.7067748560836425; -0.012301999973736542 0.7437464278187124 -0.6683486454714723], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.30000000000000115, 0.20000000000000195, 0.09999999999999792, 2.2259971643734389e-13 … 1.4988010832439613e-15, -1.2247147740396258e-15, 1.5543122344752192e-15, -9.71445146547012e-16, -1.5432100042289676e-14, -1.251776460264864e-14, -8.881784197001252e-15, 1.637578961322106e-14, 2.8782531913407183e-14, 2.000000000000001])"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"@time R, comp= findvibrationcoordinates(c6h6, deformed)"
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "b831b6a3",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"3×3 Matrix{Float64}:\n",
" 1.11022e-16 0.0 0.0\n",
" 0.0 -1.11022e-16 -1.11022e-16\n",
" -9.54098e-17 3.33067e-16 -1.11022e-16"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"R .- r"
]
},
{
"cell_type": "code",
"execution_count": 18,
"id": "2d967905",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"i = 7\n",
"comp[i] = 0.30000000000000115\n",
"i = 8\n",
"comp[i] = 0.20000000000000195\n",
"i = 9\n",
"comp[i] = 0.09999999999999792\n",
"i = 36\n",
"comp[i] = 2.000000000000001\n"
]
}
],
"source": [
"for i in 1:36 \n",
" if abs(comp[i]) > 1e-10\n",
" @show i comp[i]\n",
" end\n",
"end"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "441ee672",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Julia 1.6.0",
"language": "julia",
"name": "julia-1.6"
},
"language_info": {
"file_extension": ".jl",
"mimetype": "application/julia",
"name": "julia",
"version": "1.6.0"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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