Hi Dr. Junkermeier,<br>
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If you check with xcrysden, you will see that the first input does not reproduce a graphene layer because the carbon atoms are overlapped. I believe the first input should be something like:<br>
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&CONTROL<br>
calculation = "relax",<br>
pseudo_dir = "/app/espresso/pseudo",<br>
outdir = "/workspace/junky/lattice_top/tmp",<br>
/<br>
&SYSTEM<br>
ibrav = 4,<br>
celldm(1) = 4.80,<br>
celldm(3) = 9.6875,<br>
nat = 3,<br>
ntyp = 2,<br>
ecutwfc = 300.0,<br>
occupations = "smearing",<br>
smearing = "methfessel-paxton",<br>
degauss = 0.050,<br>
/<br>
&ELECTRONS<br>
conv_thr = 0.000001,<br>
mixing_beta = 0.30,<br>
/<br>
&IONS<br>
bfgs_ndim = 3,<br>
pot_extrapolation = "second_order",<br>
wfc_extrapolation = "second_order",<br>
/<br>
ATOMIC_SPECIES<br>
C 6.0 C.pbe-van_ak.UPF<br>
F 9.0 F.pbe-n-van.UPF<br>
ATOMIC_POSITIONS crystal<br>
C 0.0000000 0.0000000 0.000000<br>
C 0.3333333 0.6666666 0.000000<br>
F 0.0000000 0.0000000 0.050000<br>
K_POINTS automatic<br>
8 8 1 0 0 0<br>
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<div>But even using this input, the position of the F atoms is not the same compared to the second input. I don't know how many F atoms you want on top of the carbon, so I suggest you to use Xcrysden and than decide how do you exactly want your structure.<br>
I hope it helps. All best.<br>
<br>
Fabio Negreiros Ribeiro<br>
Departamento de Física da Universidade Federal de Minas Gerais - Brasil<br>
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-----Original Message-----<br>
From: Chad Junkermeier <<a href="mailto:junkermeier@bloch.nrl.navy.mil">junkermeier@bloch.nrl.navy.mil</a>><br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Sent: Wed, Mar 17, 2010 4:45 pm<br>
Subject: [Pw_forum] lattice constant from unit cell vs. from supercell<br>
<br>
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<div><span class="Apple-style-span" style="font-family: Monaco; font-size: 10px;"><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;">Hi,</span></font>
<div><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;"> I am trying to perform a set of SCF calculations on graphene with F atoms attached. If I do this using the unit cell, everything seems to work correctly, and the equilibrium lattice constant for the system seems to be correct. If, in stead, I use a 2x2 supercell I find that the equilibrium lattice constant is not the same (or even close) to the unit cell result.</span></font></div>
<div><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;"> The only differences between the two sets of calculations are the number of atoms and the value used for alat, and the number of kpoints.</span></font></div>
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<div><font class="Apple-style-span" face="Helvetica" size="3"><span class="Apple-style-span" style="font-size: 12px;">The supercell case has the following output (no analog of which is found in the unit cell case):<br>
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<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;"> Found symmetry operation: I + ( 0.0000 -0.5000 0.0000)</span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;"> This is a supercell, fractional translation are disabled</span></font></div>
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<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">Can anyone please tell me where I am going wrong in the supercell case?</span></font></div>
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<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">Thank you.</span></font></div>
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<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">Chad Junkermeier, Ph.D.</span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">NRC Post-Doctoral Fellow</span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">Naval Research Laboratory</span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">4555 Overlook Ave, S.W.</span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">Washington DC 20375</span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">Office: (202) 404-4635</span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">Fax: (202) 767-1165</span></font></div>
<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">Email: junkermeier(at)bloch.nrl.navy.mil </span></font></div>
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<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">Note that the value for celldm(3) in both of these files was computed: celldm(3) = 46.5/alat</span></font></div>
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<div><font class="Apple-style-span" size="3"><span class="Apple-style-span" style="font-size: 12px;">The commands for the unit cell case (alat = 4.80): </span></font></div>
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<div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">&CONTROL</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">calculation = "relax",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">pseudo_dir = "/app/espresso/pseudo",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">outdir = "/workspace/junky/lattice_top/tmp",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">/</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">&SYSTEM</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ibrav = 4,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">celldm(1) = 4.800,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">celldm(3) = 9.68750000000000000000,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">nat = 3,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ntyp = 2,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ecutwfc = 300.0,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">occupations = "smearing",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">smearing = "methfessel-paxton",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">degauss = 0.050,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">/</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">&ELECTRONS</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">conv_thr = 0.000001,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">mixing_beta = 0.30,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">/</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">&IONS</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">bfgs_ndim = 3,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">pot_extrapolation = "second_order",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">wfc_extrapolation = "second_order",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">/</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ATOMIC_SPECIES</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 6.0 C.pbe-van_ak.UPF</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">F 9.0 F.pbe-n-van.UPF</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ATOMIC_POSITIONS crystal</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 0.0000000 0.0000000 0.0000</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 1.00/3.00 2.00/3.00 0.0000</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">F 0.0000000 0.0000000 0.050000</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">K_POINTS automatic</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">8 8 1 0 0 0</div>
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<div><font class="Apple-style-span" face="Monaco" size="2"><span class="Apple-style-span" style="font-size: 10px;"><span class="Apple-style-span" style="font-family: Helvetica; font-size: medium;">The commands for the supercell case (alat = 4.65, celldm(1)=2*alat):</span></span></font></div>
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<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">&CONTROL</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">calculation = "relax",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">pseudo_dir = "/app/espresso/pseudo",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">outdir = "/workspace/junky/twotwoF01/tmp",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">/</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">&SYSTEM</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ibrav = 4,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">celldm(1) = 9.300,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">celldm(3) = 10.00000000000000000000,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">nat = 10,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ntyp = 2,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ecutwfc = 300.0,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">occupations = "smearing",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">smearing = "methfessel-paxton",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">degauss = 0.05,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">/</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">&ELECTRONS</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">conv_thr = 0.000001,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">mixing_beta = 0.3,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">/</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">&IONS</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">bfgs_ndim = 3,</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">pot_extrapolation = "second_order",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">wfc_extrapolation = "second_order",</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">/</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ATOMIC_SPECIES</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 6.0 C.pbe-van_ak.UPF</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">F 9.0 F.pbe-n-van.UPF</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">ATOMIC_POSITIONS crystal</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 0.0 0.0 0.0</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 0.1666666666666667 0.3333333333333333 0.0</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 0.0 0.5 0.0</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 0.1666666666666667 0.8333333333333333 0.0</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 0.5 0.0 0.0</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 0.6666666666666667 0.3333333333333333 0.0</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 0.5 0.5 0.0</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">C 0.6666666666666667 0.8333333333333333 0.0</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">F 0.0 0.0 0.05</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">F 0.1666666666666667 0.3333333333333333 0.05</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">K_POINTS automatic</div>
<div style="margin: 0px; font-family: Monaco; font-style: normal; font-variant: normal; font-weight: normal; font-size: 10px; line-height: normal; font-size-adjust: none; font-stretch: normal;">4 4 1 0 0 0</div>
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