Commit e2b2a7a5 authored by dmar's avatar dmar

Exercise-9

parent aaec79ae
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import matplotlib.pyplot as plt "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Compute correlation as:\n",
"$$ corr (t) = \\int \\dot{\\mu}(\\tau) \\cdot \\dot{\\mu}(\\tau + t) d \\tau $$\n",
" $\\tau$ will be an index that runs on all the simulation time. For every value of $\\tau$ $t$ varies and we compute the single integrand elements and sum (~integrate) it to $corr(t - \\tau)$ "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# load file reading only the columns of the derivative and skipping the first 45 rows (~ thermalization)\n",
"\n",
"D_dipole = np.loadtxt('dipolemet.traj',usecols = (4,5,6),skiprows=45,comments=' DIPOLE [Non Periodic](')\n",
"Nmax = 500\n",
"N = len(D_dipole)\n",
"timestep = 0.5 #fs\n",
"c_cm_s = 29979245800\n",
"corr_time = np.zeros(Nmax)\n",
"\n",
"for tau in range(N-Nmax):\n",
" for t in range(tau,tau+Nmax):\n",
" corr_time[t-tau] = corr_time[t-tau] + np.dot(D_dipole[tau], D_dipole[t])\n",
"\n",
"for t in range(Nmax):\n",
" corr_time[t] /= (N*(N-t))\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"fig = plt.plot(timestep*np.arange(Nmax),corr_time/corr_time[0],color='crimson', lw=2)\n",
"ax = plt.gca()\n",
"ax.set_xlabel('time')\n",
"ax.set_ylabel('correlation')\n",
"plt.savefig('METtime_corr', dpi=300,transparent=True)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"#Fmax up to 4000 cm^-1\n",
"Fmax = int((2e-15*np.pi*timestep*c_cm_s)*N*(4000/(2*np.pi)))\n",
"corr_freq = np.zeros([Fmax])\n",
"freq = np.zeros([Fmax])\n",
"\n",
"for i in range(Fmax):\n",
" omega = i*2*np.pi/N\n",
" for j in range(Nmax):\n",
" corr_freq[i] += np.cos(omega*j)*corr_time[j] \n",
" freq[i] = omega/(2e-15*np.pi*timestep*c_cm_s)\n",
"#corr_freq"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"fig = plt.plot(freq,corr_freq,color='crimson', lw=2)\n",
"ax = plt.gca()\n",
"ax.set_xlabel('frequency')\n",
"ax.set_ylabel('correlation')\n",
"plt.savefig('METfreq_corr', dpi=300,transparent=True)\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
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"cell_type": "code",
"execution_count": null,
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C C cc.spl
C H ch.spl
C N cn.spl
C O co.spl
C P cp.spl
C S cs.spl
C Zn czn.spl
H C hc.spl
H H hh.spl
H N hn.spl
H O ho.spl
H P hp.spl
H S hs.spl
H Zn hzn.spl
N C nc.spl
N H nh.spl
N N nn.spl
N O no.spl
N P np.spl
N S ns.spl
N Zn nzn.spl
O C oc.spl
O H oh.spl
O N on.spl
O O oo.spl
O P op.spl
O S os.spl
O Zn ozn.spl
P C pc.spl
P H ph.spl
P N pn.spl
P O po.spl
P P pp.spl
P S ps.spl
S C sc.spl
S H sh.spl
S N sn.spl
S O so.spl
S P sp.spl
S S ss.spl
S Zn szn.spl
Zn C znc.spl
Zn H znh.spl
Zn N znn.spl
Zn O zno.spl
Zn S zns.spl
Zn Zn znzn.spl
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C C cc.spl
C H ch.spl
C N cn.spl
C O co.spl
C P cp.spl
C S cs.spl
C Zn czn.spl
H C hc.spl
H H hh.spl
H N hn.spl
H O ho.spl
H P hp.spl
H S hs.spl
H Zn hzn.spl
N C nc.spl
N H nh.spl
N N nn.spl
N O no.spl
N P np.spl
N S ns.spl
N Zn nzn.spl
O C oc.spl
O H oh.spl
O N on.spl
O O oo.spl
O P op.spl
O S os.spl
O Zn ozn.spl
P C pc.spl
P H ph.spl
P N pn.spl
P O po.spl
P P pp.spl
P S ps.spl
S C sc.spl
S H sh.spl
S N sn.spl
S O so.spl
S P sp.spl
S S ss.spl
S Zn szn.spl
Zn C znc.spl
Zn H znh.spl
Zn N znn.spl
Zn O zno.spl
Zn S zns.spl
Zn Zn znzn.spl
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12
i = 6, E = -37.5020871543
C -0.0000167242 1.4241047795 0.0000000000
H 0.0000117730 2.4812054687 0.0000000000
C -1.2229203865 0.7083450062 0.0000000000
H -2.1515061336 1.2169258310 0.0000000000
C -1.2228578464 -0.7083475940 0.0000000000
H -2.1514706966 -1.2168780517 0.0000000000
C 0.0000162811 -1.4241567274 0.0000000000
H -0.0000143972 -2.4812584194 0.0000000000
C 1.2228735927 -0.7083177365 0.0000000000
H 2.1514569212 -1.2168987582 0.0000000000
C 1.2229035665 0.7083746665 0.0000000000
H 2.1515177018 1.2169053411 0.0000000000
6
i = 12, E = -23.9877697187
C -0.0435479100 0.6769040440 -0.0000044633
O 0.0048786826 -0.8714625537 0.0000589557
H -1.0794527472 0.9055802370 0.0000008389
H 0.9770514937 -1.1299177207 -0.0000003842
H 0.4213440524 1.0545040817 0.8763085668
H 0.4213460908 1.0545154729 -0.8763108797
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